TCGAOVARIAN: Integrated genomic analyses of ovarian carcinoma.
In bhklab/MetaGxOvarian: Transcriptomic Ovarian Cancer Datasets
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Description
A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients' lives. The Cancer Genome Atlas project has analysed messenger RNA expression, microRNA expression, promoter methylation and DNA copy number in 489 high-grade serous ovarian adenocarcinomas and the DNA sequences of exons from coding genes in 316 of these tumours. Here we report that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1, BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three microRNA subtypes, four promoter methylation subtypes and a transcriptional signature associated with survival duration, and shed new light on the impact that tumours with BRCA1/2 (BRCA1 or BRCA2) and CCNE1 aberrations have on survival. Pathway analyses suggested that homologous recombination is defective in about half of the tumours analysed, and that NOTCH and FOXM1 signalling are involved in serous ovarian cancer pathophysiology.
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experimentData(eset):
Experiment data
Experimenter name: Integrated genomic analyses of ovarian carcinoma. Nature 2011, 474:609-615.
Laboratory: Cancer Genome Atlas Research Network 2011
Contact information:
Title: Integrated genomic analyses of ovarian carcinoma.
URL:
PMIDs: 21720365
Abstract: A 179 word abstract is available. Use 'abstract' method.
Information is available on: preprocessing
notes:
platform_title:
[HT_HG-U133A] Affymetrix HT Human Genome U133A Array
platform_shorttitle:
Affymetrix HT_HG-U133A
platform_summary:
hthgu133a
platform_manufacturer:
Affymetrix
platform_distribution:
commercial
platform_accession:
GPL3921
warnings:
The following samples are likely from specimens also used in GSE26712: TCG
A.13.0725, TCGA.13.0885, TCGA.13.0887, TCGA.13.0890, TCGA.13.0886, TCGA.13
.0714, TCGA.13.0727, TCGA.13.1817, TCGA.13.1499, TCGA.13.0883
version:
2015-09-22 20:25:15
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-M27830_M_at (21260 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
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assayData: 21260 features, 578 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
21 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
557.00 290.00 3.73 3.45 4.06
---------------------------
Available sample meta-data:
---------------------------
alt_sample_name:
TCGA-01-0628-11A-01R-0362-01 TCGA-01-0630-11A-01R-0362-01
1 1
TCGA-01-0631-11A-01R-0362-01 TCGA-01-0633-11A-01R-0362-01
1 1
TCGA-01-0636-11A-01R-0362-01 TCGA-01-0637-11A-01R-0362-01
1 1
TCGA-01-0639-11A-01R-0362-01 TCGA-01-0642-11A-02R-0362-01
1 1
TCGA-04-1331-01A-01R-0434-01 TCGA-04-1332-01A-01R-0434-01
1 1
TCGA-04-1335-01A-01R-0434-01 TCGA-04-1336-01A-01R-0434-01
1 1
TCGA-04-1337-01A-01R-0434-01 TCGA-04-1338-01A-01R-0434-01
1 1
TCGA-04-1341-01A-01R-0434-01 TCGA-04-1342-01A-01R-0434-01
1 1
TCGA-04-1343-01A-01R-0434-01 TCGA-04-1346-01A-01R-0434-01
1 1
TCGA-04-1347-01A-01R-0434-01 TCGA-04-1348-01A-01R-0453-01
1 1
TCGA-04-1349-01A-01R-0453-01 TCGA-04-1350-01A-01R-0453-01
1 1
TCGA-04-1351-01A-01R-0453-01 TCGA-04-1353-01A-01R-1048-01
1 1
TCGA-04-1356-01A-01R-0453-01 TCGA-04-1357-01A-01R-0453-01
1 1
TCGA-04-1360-01A-01R-0453-01 TCGA-04-1361-01A-01R-0453-01
1 1
TCGA-04-1362-01A-01R-0453-01 TCGA-04-1364-01A-01R-0453-01
1 1
TCGA-04-1365-01A-01R-0453-01 TCGA-04-1367-01A-01R-0453-01
1 1
TCGA-04-1369-01A-02R-1048-01 TCGA-04-1371-01A-01R-0453-01
1 1
TCGA-04-1514-01A-01R-0502-01 TCGA-04-1516-01A-01R-1048-01
1 1
TCGA-04-1517-01A-01R-0538-01 TCGA-04-1519-01A-01R-0538-01
1 1
TCGA-04-1525-01A-01R-0538-01 TCGA-04-1530-01A-02R-0502-01
1 1
TCGA-04-1536-01A-01R-0538-01 TCGA-04-1542-01A-01R-0502-01
1 1
TCGA-04-1638-01A-01R-0582-01 TCGA-04-1644-01B-01R-1048-01
1 1
TCGA-04-1646-01A-01R-0582-01 TCGA-04-1648-01A-01R-0582-01
1 1
TCGA-04-1649-01A-01R-0582-01 TCGA-04-1651-01A-01R-0582-01
1 1
TCGA-04-1652-01A-01R-0582-01 TCGA-04-1654-01A-02R-0653-01
1 1
TCGA-04-1655-01A-01R-0564-01 TCGA-09-0364-01A-02R-0362-01
1 1
TCGA-09-0365-01A-02R-0362-01 TCGA-09-0366-01A-01R-0362-01
1 1
TCGA-09-0367-01A-01R-0362-01 TCGA-09-0369-01A-01R-0362-01
1 1
TCGA-09-1659-01B-01R-0538-01 TCGA-09-1661-01B-01R-0538-01
1 1
TCGA-09-1662-01A-01R-0538-01 TCGA-09-1664-01A-01R-0582-01
1 1
TCGA-09-1665-01B-01R-0538-01 TCGA-09-1666-01A-01R-0538-01
1 1
TCGA-09-1667-01C-01R-0538-01 TCGA-09-1668-01B-01R-0538-01
1 1
TCGA-09-1669-01A-01R-0538-01 TCGA-09-1670-01A-01R-0564-01
1 1
TCGA-09-1672-01A-01R-0564-01 TCGA-09-1673-01A-01R-0564-01
1 1
TCGA-09-1674-01A-01R-0564-01 TCGA-09-1675-01B-01R-0564-01
1 1
TCGA-09-2043-01A-01R-0709-01 TCGA-09-2044-01B-01R-0709-01
1 1
TCGA-09-2045-01A-01R-0709-01 TCGA-09-2048-01A-01R-0709-01
1 1
TCGA-09-2049-01D-01R-0709-01 TCGA-09-2050-01A-01R-0709-01
1 1
TCGA-09-2051-01A-01R-0709-01 TCGA-09-2053-01C-01R-0668-01
1 1
TCGA-09-2054-01A-01R-0668-01 TCGA-09-2055-01B-01R-0709-01
1 1
TCGA-09-2056-01B-01R-0668-01 TCGA-10-0925-01B-01R-0653-01
1 1
TCGA-10-0926-01A-01R-0404-01 TCGA-10-0927-01A-02R-0404-01
1 1
TCGA-10-0928-01A-02R-0404-01 TCGA-10-0930-01A-02R-0404-01
1 1
TCGA-10-0931-01A-01R-0404-01 TCGA-10-0933-01A-01R-0404-01
1 1
TCGA-10-0934-01A-02R-0404-01 TCGA-10-0935-01A-02R-0404-01
1 1
TCGA-10-0936-01A-01R-0404-01 TCGA-10-0937-01A-02R-0404-01
1 1
TCGA-10-0938-01A-02R-0404-01 TCGA-13-0714-01A-01R-0362-01
1 1
TCGA-13-0717-01A-01R-0362-01 TCGA-13-0720-01A-01R-0362-01
1 1
TCGA-13-0723-01A-02R-0362-01 TCGA-13-0724-01A-01R-0362-01
1 1
(Other) NA's
479 1
unique_patient_ID:
TCGA-01-0628 TCGA-01-0630 TCGA-01-0631 TCGA-01-0633 TCGA-01-0636 TCGA-01-0637
1 1 1 1 1 1
TCGA-01-0639 TCGA-01-0642 TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336
1 1 1 1 1 1
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346
1 1 1 1 1 1
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353
1 1 1 1 1 1
TCGA-04-1356 TCGA-04-1357 TCGA-04-1360 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364
1 1 1 1 1 1
TCGA-04-1365 TCGA-04-1367 TCGA-04-1369 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516
1 1 1 1 1 1
TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542
1 1 1 1 1 1
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651
1 1 1 1 1 1
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366
1 1 1 1 1 1
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664
1 1 1 1 1 1
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670
1 1 1 1 1 1
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044
1 1 1 1 1 1
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053
1 1 1 1 1 1
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927
1 1 1 1 1 1
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935
1 1 1 1 1 1
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720
1 1 1 1 1 1
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 (Other)
1 1 1 479
sample_type:
adjacentnormal tumor
8 570
histological_type:
ser NA's
568 10
primarysite:
other ov NA's
4 564 10
summarygrade:
high low NA's
480 75 23
summarystage:
early late NA's
43 520 15
tumorstage:
1 2 3 4 NA's
16 27 436 84 15
substage:
b c NA's
31 448 99
grade:
1 2 3 4 NA's
6 69 479 1 23
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
26.00 51.00 59.00 59.70 68.25 89.00 10
pltx:
n y NA's
19 492 67
tax:
n y NA's
43 468 67
neo:
n NA's
511 67
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
8.0 238.2 443.5 623.7 812.0 5480.0 56
recurrence_status:
norecurrence recurrence
279 299
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
8 349 881 1010 1446 5480 21
vital_status:
deceased living NA's
290 270 18
site_of_tumor_first_recurrence:
locoregional locoregional_plus_metastatic
153 3
metastasis NA's
143 279
primary_therapy_outcome_success:
completeresponse partialresponse progressivedisease stabledisease
318 65 41 30
NA's
124
debulking:
optimal suboptimal NA's
367 140 71
percent_normal_cells:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.385 0.000 55.000 19
percent_stromal_cells:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 5.00 10.00 12.85 20.00 70.00 25
percent_tumor_cells:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 75.00 85.00 80.64 90.00 100.00 22
batch:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.00 13.00 17.00 18.55 22.00 40.00 1
uncurated_author_metadata:
age_at_initial_pathologic_diagnosis: 26///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: 30c7efdd-5a86-4418-a33c-a5d27fe56e42///days_to_birth: -9760///days_to_initial_pathologic_diagnosis: 0///ethnicity: NOT HISPANIC OR LATINO///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: YES///neoplasm_histologic_grade: G1///patient_id: 2540///pretreatment_history: NO///race: WHITE///residual_tumor: R1///tissue_source_site: 36///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: >20 mm///tumor_stage: IIIC///tumor_tissue_site: OVARY///venous_invasion: YES///year_of_initial_pathologic_diagnosis: 2008///additional_chemo_therapy: YES///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NA///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: e4383d0b-9cc4-4fb5-a4a1-312928dd2e34///chemo_therapy: YES///day_of_form_completion: 18///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: NA///days_to_last_followup: 724///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: 665///eastern_cancer_oncology_group: 0///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 8///performance_status_scale_timing: Pre-Operative///person_neoplasm_cancer_status: WITH TUMOR///primary_therapy_outcome_success: Complete Response///progression_determined_by: Imaging Study///progression_determined_by_notes: CT///radiation_therapy: NO///site_of_tumor_first_recurrence: Locoregional and Metastasis///targeted_molecular_therapy: NO///vital_status: LIVING///year_of_form_completion: 2010///unique_patient_ID: TCGA-36-2540///batch: 40///Extract.Name: TCGA-36-2540-01A-01R-1048-01
1
age_at_initial_pathologic_diagnosis: 30///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: da274941-3edd-420b-9262-bbd959923c67///days_to_birth: -11145///days_to_initial_pathologic_diagnosis: 0///ethnicity: NA///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: NO///neoplasm_histologic_grade: G3///patient_id: 1946///pretreatment_history: NO///race: NA///residual_tumor: NA///tissue_source_site: 31///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: No Macroscopic disease///tumor_stage: IIIC///tumor_tissue_site: OVARY///venous_invasion: YES///year_of_initial_pathologic_diagnosis: 2006///additional_chemo_therapy: YES///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NO///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: 5a829c07-1749-4281-9d01-caab3b1caf7c///chemo_therapy: YES///day_of_form_completion: 20///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: NA///days_to_last_followup: 918///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: 664///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 10///performance_status_scale_timing: NA///person_neoplasm_cancer_status: WITH TUMOR///primary_therapy_outcome_success: NA///progression_determined_by: Physical Examination///progression_determined_by_notes: NA///radiation_therapy: NO///site_of_tumor_first_recurrence: Loco-Regional///targeted_molecular_therapy: NO///vital_status: LIVING///year_of_form_completion: 2009///unique_patient_ID: TCGA-31-1946///batch: 21///Extract.Name: TCGA-31-1946-01A-01R-0653-01
1
age_at_initial_pathologic_diagnosis: 34///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: f9793a4b-c0e7-4475-bf80-69543b7ee2f6///days_to_birth: -12772///days_to_initial_pathologic_diagnosis: 0///ethnicity: NA///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: NA///neoplasm_histologic_grade: G3///patient_id: 1416///pretreatment_history: NO///race: WHITE///residual_tumor: NA///tissue_source_site: 24///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: 1-10 mm///tumor_stage: IV///tumor_tissue_site: OVARY///venous_invasion: NA///year_of_initial_pathologic_diagnosis: 2008///additional_chemo_therapy: NO///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NA///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: cf7ad1d4-c805-41b7-8c74-2e09210bfd7e///chemo_therapy: YES///day_of_form_completion: 1///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: NA///days_to_last_followup: 194///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: NA///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 4///performance_status_scale_timing: NA///person_neoplasm_cancer_status: TUMOR FREE///primary_therapy_outcome_success: Complete Response///progression_determined_by: NA///progression_determined_by_notes: NA///radiation_therapy: NO///site_of_tumor_first_recurrence: NA///targeted_molecular_therapy: NO///vital_status: LIVING///year_of_form_completion: 2009///unique_patient_ID: TCGA-24-1416///batch: 14///Extract.Name: TCGA-24-1416-01A-01R-0477-01
1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
(Other)
479
duplicates:
Length Class Mode
578 character character
Value
An expression set
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Description Format Details Value
Description
A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients' lives. The Cancer Genome Atlas project has analysed messenger RNA expression, microRNA expression, promoter methylation and DNA copy number in 489 high-grade serous ovarian adenocarcinomas and the DNA sequences of exons from coding genes in 316 of these tumours. Here we report that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1, BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three microRNA subtypes, four promoter methylation subtypes and a transcriptional signature associated with survival duration, and shed new light on the impact that tumours with BRCA1/2 (BRCA1 or BRCA2) and CCNE1 aberrations have on survival. Pathway analyses suggested that homologous recombination is defective in about half of the tumours analysed, and that NOTCH and FOXM1 signalling are involved in serous ovarian cancer pathophysiology.
Format
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 | experimentData(eset):
Experiment data
Experimenter name: Integrated genomic analyses of ovarian carcinoma. Nature 2011, 474:609-615.
Laboratory: Cancer Genome Atlas Research Network 2011
Contact information:
Title: Integrated genomic analyses of ovarian carcinoma.
URL:
PMIDs: 21720365
Abstract: A 179 word abstract is available. Use 'abstract' method.
Information is available on: preprocessing
notes:
platform_title:
[HT_HG-U133A] Affymetrix HT Human Genome U133A Array
platform_shorttitle:
Affymetrix HT_HG-U133A
platform_summary:
hthgu133a
platform_manufacturer:
Affymetrix
platform_distribution:
commercial
platform_accession:
GPL3921
warnings:
The following samples are likely from specimens also used in GSE26712: TCG
A.13.0725, TCGA.13.0885, TCGA.13.0887, TCGA.13.0890, TCGA.13.0886, TCGA.13
.0714, TCGA.13.0727, TCGA.13.1817, TCGA.13.1499, TCGA.13.0883
version:
2015-09-22 20:25:15
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-M27830_M_at (21260 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
|
Details
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 | assayData: 21260 features, 578 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
21 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
557.00 290.00 3.73 3.45 4.06
---------------------------
Available sample meta-data:
---------------------------
alt_sample_name:
TCGA-01-0628-11A-01R-0362-01 TCGA-01-0630-11A-01R-0362-01
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TCGA-01-0631-11A-01R-0362-01 TCGA-01-0633-11A-01R-0362-01
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TCGA-01-0636-11A-01R-0362-01 TCGA-01-0637-11A-01R-0362-01
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TCGA-01-0639-11A-01R-0362-01 TCGA-01-0642-11A-02R-0362-01
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TCGA-04-1331-01A-01R-0434-01 TCGA-04-1332-01A-01R-0434-01
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TCGA-04-1335-01A-01R-0434-01 TCGA-04-1336-01A-01R-0434-01
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TCGA-04-1337-01A-01R-0434-01 TCGA-04-1338-01A-01R-0434-01
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TCGA-04-1341-01A-01R-0434-01 TCGA-04-1342-01A-01R-0434-01
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TCGA-04-1343-01A-01R-0434-01 TCGA-04-1346-01A-01R-0434-01
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TCGA-04-1347-01A-01R-0434-01 TCGA-04-1348-01A-01R-0453-01
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TCGA-04-1349-01A-01R-0453-01 TCGA-04-1350-01A-01R-0453-01
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TCGA-04-1351-01A-01R-0453-01 TCGA-04-1353-01A-01R-1048-01
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TCGA-04-1356-01A-01R-0453-01 TCGA-04-1357-01A-01R-0453-01
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TCGA-04-1360-01A-01R-0453-01 TCGA-04-1361-01A-01R-0453-01
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TCGA-04-1362-01A-01R-0453-01 TCGA-04-1364-01A-01R-0453-01
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TCGA-04-1365-01A-01R-0453-01 TCGA-04-1367-01A-01R-0453-01
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TCGA-04-1369-01A-02R-1048-01 TCGA-04-1371-01A-01R-0453-01
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TCGA-04-1514-01A-01R-0502-01 TCGA-04-1516-01A-01R-1048-01
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TCGA-04-1517-01A-01R-0538-01 TCGA-04-1519-01A-01R-0538-01
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TCGA-04-1525-01A-01R-0538-01 TCGA-04-1530-01A-02R-0502-01
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TCGA-04-1536-01A-01R-0538-01 TCGA-04-1542-01A-01R-0502-01
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TCGA-04-1638-01A-01R-0582-01 TCGA-04-1644-01B-01R-1048-01
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TCGA-04-1646-01A-01R-0582-01 TCGA-04-1648-01A-01R-0582-01
1 1
TCGA-04-1649-01A-01R-0582-01 TCGA-04-1651-01A-01R-0582-01
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TCGA-04-1652-01A-01R-0582-01 TCGA-04-1654-01A-02R-0653-01
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TCGA-04-1655-01A-01R-0564-01 TCGA-09-0364-01A-02R-0362-01
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TCGA-09-0365-01A-02R-0362-01 TCGA-09-0366-01A-01R-0362-01
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TCGA-09-0367-01A-01R-0362-01 TCGA-09-0369-01A-01R-0362-01
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TCGA-09-1659-01B-01R-0538-01 TCGA-09-1661-01B-01R-0538-01
1 1
TCGA-09-1662-01A-01R-0538-01 TCGA-09-1664-01A-01R-0582-01
1 1
TCGA-09-1665-01B-01R-0538-01 TCGA-09-1666-01A-01R-0538-01
1 1
TCGA-09-1667-01C-01R-0538-01 TCGA-09-1668-01B-01R-0538-01
1 1
TCGA-09-1669-01A-01R-0538-01 TCGA-09-1670-01A-01R-0564-01
1 1
TCGA-09-1672-01A-01R-0564-01 TCGA-09-1673-01A-01R-0564-01
1 1
TCGA-09-1674-01A-01R-0564-01 TCGA-09-1675-01B-01R-0564-01
1 1
TCGA-09-2043-01A-01R-0709-01 TCGA-09-2044-01B-01R-0709-01
1 1
TCGA-09-2045-01A-01R-0709-01 TCGA-09-2048-01A-01R-0709-01
1 1
TCGA-09-2049-01D-01R-0709-01 TCGA-09-2050-01A-01R-0709-01
1 1
TCGA-09-2051-01A-01R-0709-01 TCGA-09-2053-01C-01R-0668-01
1 1
TCGA-09-2054-01A-01R-0668-01 TCGA-09-2055-01B-01R-0709-01
1 1
TCGA-09-2056-01B-01R-0668-01 TCGA-10-0925-01B-01R-0653-01
1 1
TCGA-10-0926-01A-01R-0404-01 TCGA-10-0927-01A-02R-0404-01
1 1
TCGA-10-0928-01A-02R-0404-01 TCGA-10-0930-01A-02R-0404-01
1 1
TCGA-10-0931-01A-01R-0404-01 TCGA-10-0933-01A-01R-0404-01
1 1
TCGA-10-0934-01A-02R-0404-01 TCGA-10-0935-01A-02R-0404-01
1 1
TCGA-10-0936-01A-01R-0404-01 TCGA-10-0937-01A-02R-0404-01
1 1
TCGA-10-0938-01A-02R-0404-01 TCGA-13-0714-01A-01R-0362-01
1 1
TCGA-13-0717-01A-01R-0362-01 TCGA-13-0720-01A-01R-0362-01
1 1
TCGA-13-0723-01A-02R-0362-01 TCGA-13-0724-01A-01R-0362-01
1 1
(Other) NA's
479 1
unique_patient_ID:
TCGA-01-0628 TCGA-01-0630 TCGA-01-0631 TCGA-01-0633 TCGA-01-0636 TCGA-01-0637
1 1 1 1 1 1
TCGA-01-0639 TCGA-01-0642 TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336
1 1 1 1 1 1
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346
1 1 1 1 1 1
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353
1 1 1 1 1 1
TCGA-04-1356 TCGA-04-1357 TCGA-04-1360 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364
1 1 1 1 1 1
TCGA-04-1365 TCGA-04-1367 TCGA-04-1369 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516
1 1 1 1 1 1
TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542
1 1 1 1 1 1
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651
1 1 1 1 1 1
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366
1 1 1 1 1 1
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664
1 1 1 1 1 1
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670
1 1 1 1 1 1
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044
1 1 1 1 1 1
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053
1 1 1 1 1 1
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927
1 1 1 1 1 1
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935
1 1 1 1 1 1
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720
1 1 1 1 1 1
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 (Other)
1 1 1 479
sample_type:
adjacentnormal tumor
8 570
histological_type:
ser NA's
568 10
primarysite:
other ov NA's
4 564 10
summarygrade:
high low NA's
480 75 23
summarystage:
early late NA's
43 520 15
tumorstage:
1 2 3 4 NA's
16 27 436 84 15
substage:
b c NA's
31 448 99
grade:
1 2 3 4 NA's
6 69 479 1 23
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
26.00 51.00 59.00 59.70 68.25 89.00 10
pltx:
n y NA's
19 492 67
tax:
n y NA's
43 468 67
neo:
n NA's
511 67
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
8.0 238.2 443.5 623.7 812.0 5480.0 56
recurrence_status:
norecurrence recurrence
279 299
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
8 349 881 1010 1446 5480 21
vital_status:
deceased living NA's
290 270 18
site_of_tumor_first_recurrence:
locoregional locoregional_plus_metastatic
153 3
metastasis NA's
143 279
primary_therapy_outcome_success:
completeresponse partialresponse progressivedisease stabledisease
318 65 41 30
NA's
124
debulking:
optimal suboptimal NA's
367 140 71
percent_normal_cells:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.385 0.000 55.000 19
percent_stromal_cells:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 5.00 10.00 12.85 20.00 70.00 25
percent_tumor_cells:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 75.00 85.00 80.64 90.00 100.00 22
batch:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.00 13.00 17.00 18.55 22.00 40.00 1
uncurated_author_metadata:
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1
age_at_initial_pathologic_diagnosis: 30///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: da274941-3edd-420b-9262-bbd959923c67///days_to_birth: -11145///days_to_initial_pathologic_diagnosis: 0///ethnicity: NA///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: NO///neoplasm_histologic_grade: G3///patient_id: 1946///pretreatment_history: NO///race: NA///residual_tumor: NA///tissue_source_site: 31///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: No Macroscopic disease///tumor_stage: IIIC///tumor_tissue_site: OVARY///venous_invasion: YES///year_of_initial_pathologic_diagnosis: 2006///additional_chemo_therapy: YES///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NO///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: 5a829c07-1749-4281-9d01-caab3b1caf7c///chemo_therapy: YES///day_of_form_completion: 20///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: NA///days_to_last_followup: 918///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: 664///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 10///performance_status_scale_timing: NA///person_neoplasm_cancer_status: WITH TUMOR///primary_therapy_outcome_success: NA///progression_determined_by: Physical Examination///progression_determined_by_notes: NA///radiation_therapy: NO///site_of_tumor_first_recurrence: Loco-Regional///targeted_molecular_therapy: NO///vital_status: LIVING///year_of_form_completion: 2009///unique_patient_ID: TCGA-31-1946///batch: 21///Extract.Name: TCGA-31-1946-01A-01R-0653-01
1
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1
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1
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1
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1
age_at_initial_pathologic_diagnosis: 37///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: fdd4adb8-9295-480a-9352-305b5eb51187///days_to_birth: -13606///days_to_initial_pathologic_diagnosis: 0///ethnicity: NOT HISPANIC OR LATINO///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: NA///neoplasm_histologic_grade: G2///patient_id: 2408///pretreatment_history: NO///race: WHITE///residual_tumor: NA///tissue_source_site: 25///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: 1-10 mm///tumor_stage: IV///tumor_tissue_site: OVARY///venous_invasion: NA///year_of_initial_pathologic_diagnosis: 2005///additional_chemo_therapy: NA///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NA///additional_surgery_metastatic_procedure: YES///bcr_followup_uuid: f82208f0-6255-4dd7-8523-c0c9da6e0800///chemo_therapy: YES///day_of_form_completion: 5///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: 333///days_to_death: 942///days_to_last_followup: 942///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: 333///eastern_cancer_oncology_group: NA///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 1///performance_status_scale_timing: NA///person_neoplasm_cancer_status: WITH TUMOR///primary_therapy_outcome_success: Partial Response///progression_determined_by: First Seen At Further Surgery///progression_determined_by_notes: NA///radiation_therapy: NO///site_of_tumor_first_recurrence: Metastasis///targeted_molecular_therapy: NO///vital_status: DECEASED///year_of_form_completion: 2010///unique_patient_ID: TCGA-25-2408///batch: 24///Extract.Name: TCGA-25-2408-01A-01R-0709-01
1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
age_at_initial_pathologic_diagnosis: 49///anatomic_organ_subdivision: Bilateral///bcr_patient_uuid: 09c77947-a333-4392-b18d-a6c1f08764a1///days_to_birth: -18227///days_to_initial_pathologic_diagnosis: 0///ethnicity: NA///gender: FEMALE///gynecologic_figo_staging_system: NA///histological_type: Serous Cystadenocarcinoma///icd_10: NA///icd_o_3_histology: 8441/3///icd_o_3_site: C56.9///informed_consent_verified: YES///initial_pathologic_diagnosis_method: Tumor resection///jewish_origin: NA///lymphatic_invasion: YES///neoplasm_histologic_grade: G3///patient_id: 1842///pretreatment_history: NO///race: WHITE///residual_tumor: NA///tissue_source_site: 24///tumor_histologic_subtype: Cystadenocarcinoma///tumor_residual_disease: 1-10 mm///tumor_stage: IIIC///tumor_tissue_site: OVARY///venous_invasion: NA///year_of_initial_pathologic_diagnosis: 2009///additional_chemo_therapy: NO///additional_drug_therapy: NO///additional_immuno_therapy: NO///additional_pharmaceutical_therapy: NO///additional_radiation_therapy: NO///additional_surgery_locoregional_procedure: NA///additional_surgery_metastatic_procedure: NA///bcr_followup_uuid: ea813aa8-df86-407b-aea1-092fb2c8608e///chemo_therapy: YES///day_of_form_completion: 2///days_to_additional_surgery_locoregional_procedure: NA///days_to_additional_surgery_metastatic_procedure: NA///days_to_death: NA///days_to_last_followup: 253///days_to_new_tumor_event_after_initial_treatment: NA///days_to_tumor_progression: NA///days_to_tumor_recurrence: NA///eastern_cancer_oncology_group: 0///followup_case_report_form_submission_reason: NA///hormonal_therapy: NO///immuno_therapy: NO///karnofsky_performance_score: NA///month_of_form_completion: 6///performance_status_scale_timing: Other///person_neoplasm_cancer_status: TUMOR FREE///primary_therapy_outcome_success: Complete Response///progression_determined_by: NA///progression_determined_by_notes: NA///radiation_therapy: NO///site_of_tumor_first_recurrence: NA///targeted_molecular_therapy: YES///vital_status: LIVING///year_of_form_completion: 2009///unique_patient_ID: TCGA-24-1842///batch: 19///Extract.Name: TCGA-24-1842-01A-01R-0582-01
1
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An expression set
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