Description Format Details Value
Advanced stage papillary serous tumors of the ovary are responsible for the majority of ovarian cancer deaths, yet the molecular determinants modulating patient survival are poorly characterized. Here, we identify and validate a prognostic gene expression signature correlating with survival in a series of microdissected serous ovarian tumors. Independent evaluation confirmed the association of a prognostic gene microfibril-associated glycoprotein 2 (MAGP2) with poor prognosis, whereas in vitro mechanistic analyses demonstrated its ability to prolong tumor cell survival and stimulate endothelial cell motility and survival via the alpha(V)beta(3) integrin receptor. Increased MAGP2 expression correlated with microvessel density suggesting a proangiogenic role in vivo. Thus, MAGP2 may serve as a survival-associated target.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | experimentData(eset):
Experiment data
Experimenter name: Mok SC, Bonome T, Vathipadiekal V, Bell A, Johnson ME, Wong KK, Park DC, Hao K, Yip DK, Donninger H, Ozbun L, Samimi G, Brady J, Randonovich M, Pise-Masison CA, Barrett JC, Wong WH, Welch WR, Berkowitz RS, Birrer MJ.A gene signature predictive for outcome in advanced ovarian cancer identifies a survival factor: microfibril-associated glycoprotein 2. Cancer Cell. 2009 Dec 8; 16(6):521-32.
Laboratory: Mok, Birrer 2009
Contact information:
Title: A gene signature predictive for outcome in advanced ovarian cancer identifies a survival factor: microfibril-associated glycoprotein 2.
URL:
PMIDs: 19962670
Abstract: A 110 word abstract is available. Use 'abstract' method.
Information is available on: preprocessing
notes:
platform_title:
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
platform_shorttitle:
Affymetrix HG-U133Plus2
platform_summary:
hgu133plus2
platform_manufacturer:
Affymetrix|Operon
platform_distribution:
commercial|non-commercial
platform_accession:
GPL570|GPL9216
version:
2015-09-22 19:21:25
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(42447 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
|
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 | assayData: 42447 features, 63 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
10 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
53.00 41.00 2.05 1.48 3.70
---------------------------
Available sample meta-data:
---------------------------
alt_sample_name:
Min. 1st Qu. Median Mean 3rd Qu. Max.
312.0 395.0 694.0 893.3 1040.0 2237.0
sample_type:
healthy tumor
10 53
histological_type:
ser NA's
53 10
primarysite:
ov
63
summarygrade:
high NA's
53 10
summarystage:
late NA's
53 10
tumorstage:
3 NA's
53 10
grade:
3 NA's
53 10
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
150 450 630 1212 1440 4500 10
vital_status:
deceased living NA's
41 12 10
debulking:
optimal
63
percent_normal_cells:
0
63
percent_stromal_cells:
0
63
percent_tumor_cells:
100
63
batch:
2004-03-12 2004-04-08 2004-04-09 2004-07-20 2004-08-12 2004-08-13 2004-09-30
20 6 9 11 10 1 6
uncurated_author_metadata:
title: Normal Ovary, 2008///geo_accession: GSM462643///status: Public on Oct 17 2009///submission_date: Oct 16 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: normal ovarian surface epithelium (OSE)///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian surface epithelium (OSE)///characteristics_ch1.1: ///characteristics_ch1.2: ///characteristics_ch1.3: ///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from normal ovary.///description.1: HOSE2008///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Normal Ovary, 2061///geo_accession: GSM462644///status: Public on Oct 17 2009///submission_date: Oct 16 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: normal ovarian surface epithelium (OSE)///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian surface epithelium (OSE)///characteristics_ch1.1: ///characteristics_ch1.2: ///characteristics_ch1.3: ///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from normal ovary.///description.1: HOSE2061///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Normal Ovary, 2064///geo_accession: GSM462645///status: Public on Oct 17 2009///submission_date: Oct 16 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: normal ovarian surface epithelium (OSE)///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian surface epithelium (OSE)///characteristics_ch1.1: ///characteristics_ch1.2: ///characteristics_ch1.3: ///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from normal ovary.///description.1: HOSE2064///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Normal Ovary, 2085///geo_accession: GSM462646///status: Public on Oct 17 2009///submission_date: Oct 16 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: normal ovarian surface epithelium (OSE)///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian surface epithelium (OSE)///characteristics_ch1.1: ///characteristics_ch1.2: ///characteristics_ch1.3: ///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from normal ovary.///description.1: HOSE2085///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Normal Ovary, 2225///geo_accession: GSM462647///status: Public on Oct 17 2009///submission_date: Oct 16 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: normal ovarian surface epithelium (OSE)///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian surface epithelium (OSE)///characteristics_ch1.1: ///characteristics_ch1.2: ///characteristics_ch1.3: ///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from normal ovary.///description.1: HOSE2225///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Normal Ovary, 2226///geo_accession: GSM462648///status: Public on Oct 17 2009///submission_date: Oct 16 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: normal ovarian surface epithelium (OSE)///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian surface epithelium (OSE)///characteristics_ch1.1: ///characteristics_ch1.2: ///characteristics_ch1.3: ///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from normal ovary.///description.1: HOSE2226///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Normal Ovary, 2228///geo_accession: GSM462649///status: Public on Oct 17 2009///submission_date: Oct 16 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: normal ovarian surface epithelium (OSE)///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian surface epithelium (OSE)///characteristics_ch1.1: ///characteristics_ch1.2: ///characteristics_ch1.3: ///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from normal ovary.///description.1: HOSE2228///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Normal Ovary, 2230///geo_accession: GSM462650///status: Public on Oct 17 2009///submission_date: Oct 16 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: normal ovarian surface epithelium (OSE)///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian surface epithelium (OSE)///characteristics_ch1.1: ///characteristics_ch1.2: ///characteristics_ch1.3: ///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from normal ovary.///description.1: HOSE2230///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Normal Ovary, 2234///geo_accession: GSM462651///status: Public on Oct 17 2009///submission_date: Oct 16 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: normal ovarian surface epithelium (OSE)///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian surface epithelium (OSE)///characteristics_ch1.1: ///characteristics_ch1.2: ///characteristics_ch1.3: ///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from normal ovary.///description.1: HOSE2234///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Normal Ovary, 2237///geo_accession: GSM462652///status: Public on Oct 17 2009///submission_date: Oct 16 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: normal ovarian surface epithelium (OSE)///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian surface epithelium (OSE)///characteristics_ch1.1: ///characteristics_ch1.2: ///characteristics_ch1.3: ///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from normal ovary.///description.1: HOSE2237///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 1109///geo_accession: GSM461390///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 34 (A)///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 1109///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 1214///geo_accession: GSM461391///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 17///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 1214///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 1231///geo_accession: GSM461367///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 15///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 1231///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 1562///geo_accession: GSM461368///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 19 (A)///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 1562///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 1660///geo_accession: GSM461369///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 15 (A)///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 1660///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 1993///geo_accession: GSM461400///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 11 (A)///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 1993///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 312///geo_accession: GSM461379///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 48///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 312///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 317///geo_accession: GSM461348///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 150 (A)///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 317///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 321///geo_accession: GSM461380///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 45///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 321///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 324///geo_accession: GSM461373///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 59///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 324///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 332///geo_accession: GSM461349///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 7///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 332///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 345///geo_accession: GSM461392///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 18///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 345///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 349///geo_accession: GSM461350///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 144 (A)///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 349///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 351///geo_accession: GSM461351///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 142 (A)///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 351///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 358///geo_accession: GSM461393///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 21///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 358///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 367///geo_accession: GSM461381///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 16///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 367///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 377///geo_accession: GSM461374///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 12///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 377///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 380///geo_accession: GSM461375///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 57///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 380///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 386///geo_accession: GSM461352///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 95///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 386///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 388///geo_accession: GSM461353///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 132 (A)///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 388///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 389///geo_accession: GSM461354///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 13///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 389///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 394///geo_accession: GSM461382///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 16///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 394///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 396///geo_accession: GSM461376///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 21///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 396///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 402///geo_accession: GSM461355///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 8///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 402///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 410///geo_accession: GSM461356///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 150 (A)///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 410///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 412///geo_accession: GSM461357///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 113///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 412///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 434///geo_accession: GSM461358///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 72///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 434///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 443///geo_accession: GSM461377///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 111///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 443///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 461///geo_accession: GSM461394///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 32///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 461///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 467///geo_accession: GSM461359///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 11///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 467///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 477///geo_accession: GSM461383///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 21///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 477///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 486///geo_accession: GSM461395///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 21///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 486///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 629///geo_accession: GSM461360///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 50 (A)///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 629///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 631///geo_accession: GSM461396///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 30///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 631///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 656///geo_accession: GSM461384///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 25///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 656///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 662///geo_accession: GSM461370///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 23///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 662///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 692///geo_accession: GSM461397///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 35///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 692///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 694///geo_accession: GSM461385///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 33///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 694///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 702///geo_accession: GSM461361///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 13///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 702///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 714///geo_accession: GSM461362///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 8///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 714///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 715///geo_accession: GSM461386///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 33///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 715///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 718///geo_accession: GSM461398///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 26///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 718///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 744///geo_accession: GSM461378///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 14///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 744///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 765///geo_accession: GSM461363///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 12///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 765///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 778///geo_accession: GSM461399///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 16///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 778///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 780///geo_accession: GSM461364///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 11///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 780///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 786///geo_accession: GSM461387///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 48 (A)///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 786///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 794///geo_accession: GSM461388///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 15///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 794///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 799///geo_accession: GSM461365///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 5///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 799///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 800///geo_accession: GSM461371///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 36///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 800///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 872///geo_accession: GSM461366///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 9///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 872///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 934///geo_accession: GSM461372///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 36 (A)///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 934///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
title: Ovarian Tumor, 970///geo_accession: GSM461389///status: Public on Oct 17 2009///submission_date: Oct 11 2009///last_update_date: Jan 19 2011///type: RNA///channel_count: 1///source_name_ch1: papillary serous ovarian adenocarcinoma///organism_ch1: Homo sapiens///characteristics_ch1: tissue: papillary serous ovarian adenocarcinoma///characteristics_ch1.1: tumor stage: late///characteristics_ch1.2: tumor grade: high///characteristics_ch1.3: surv data: 18///treatment_protocol_ch1: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.///molecule_ch1: total RNA///extract_protocol_ch1: RNeasy Micro Kit according to the manufacturers protocol (Qiagen Inc., Valencia, CA).///label_ch1: biotin///label_protocol_ch1: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.///taxid_ch1: 9606///hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).///scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).///description: Gene expression data from tumor.///description.1: 970///data_processing: Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software. A modified semi-supervised method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90
1
duplicates:
GSE18520.GSE18520_GSM462649
1
GSE18520.GSE18520_GSM462649///GSE18520.GSE18520_GSM462650
1
GSE18520.GSE18520_GSM462650
1
NA's
60
|
An expression set
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