DAVIDGenes-class: class "DAVIDGenes
In RDAVIDWebService: An R Package for retrieving data from DAVID into R objects using Web Services API.
Description
Type
Extends
Slots
Methods
Author(s)
References
See Also
Examples
Description
This class represents the output of "Show Genes Result"
of DAVID. It is an heir of DAVIDResult in the conceptual
way, and also a data.frame with additional features, such
as identifying the unique and duplicate ids, searching
for genes with a given id, etc.
Type
This class is a "Concrete" one.
Extends
-
DAVIDResult in the conceptual way.
-
data.frame in order to extend the basic
features.
Slots
none additional to the ones inherited from DAVIDResult
and data.frame classes.
Methods
validsignature(object="DAVIDGenes"):
logical which checks for data.frame name (ID, Name)
presence.
DAVIDGenessignature(object="character"):
constructor with the name of the .tab file report to
load.
DAVIDGenessignature(object="data.frame"):
data.frame already loaded to use when constructing the
object.
idssignature(object="DAVIDGenes"):
character vector with gene submitted ids.
Author(s)
Cristobal Fresno and Elmer A Fernandez
References
The Database for Annotation,
Visualization and Integrated Discovery
(david.abcc.ncifcrf.gov)
Huang, D. W.; Sherman, B.
T.; Tan, Q.; Kir, J.; Liu, D.; Bryant, D.; Guo, Y.;
Stephens, R.; Baseler, M. W.; Lane, H. C. & Lempicki, R.
A. DAVID Bioinformatics Resources: expanded annotation
database and novel algorithms to better extract biology
from large gene lists. Nucleic Acids Res, Laboratory of
Immunopathogenesis and Bioinformatics, SAIC-Frederick,
Inc., National Cancer Institute at Frederick, MD 21702,
USA., 2007, 35, W169-W175
See Also
Other DAVIDGenes:
DAVIDFunctionalAnnotationChart,
DAVIDFunctionalAnnotationChart,
DAVIDFunctionalAnnotationChart,
DAVIDFunctionalAnnotationTable,
DAVIDFunctionalAnnotationTable,
DAVIDFunctionalAnnotationTable,
DAVIDGODag, DAVIDGODag,
DAVIDGeneCluster,
DAVIDGeneCluster, DAVIDGenes,
DAVIDGenes, DAVIDGenes,
DAVIDTermCluster,
DAVIDTermCluster, as,
as, as, genes,
genes, genes,
genes, ids,
ids, ids, ids,
ids, initialize,
initialize, initialize,
initialize, initialize,
initialize, initialize
Examples
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
{
##Load Show Gene List file report for the input demo file 1, using data
##function. Then, create a DAVIDGenes object using the loaded data.frame
##geneList1. In addition, the user can use the file name of the downloaded
##file report.
data(geneList1)
davidGenes1<-DAVIDGenes(geneList1)
##Now we can inspect davidGenes1 as it was an common data.frame
head(davidGenes1)
##Additional getters for this object are also available, to obtain the
##different columns: ids, genes and species.
ids(davidGenes1)
genes(davidGenes1)
species(davidGenes1)
##Or even look up for a particular gene id, which will return only the
##matched ones.
genes(davidGenes1, ids=c("38926_at", "35367_at", "no match"))
##Obtain the genes with duplicate manufacturer ids or just the genes that
##do not have duplicate ids (uniqueIds).
duplicateIds(davidGenes1)
uniqueIds(davidGenes1)
}
Example output
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: GOstats
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: Category
Loading required package: stats4
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Attaching package: 'GOstats'
The following object is masked from 'package:AnnotationDbi':
makeGOGraph
Loading required package: ggplot2
Attaching package: 'RDAVIDWebService'
The following object is masked from 'package:AnnotationDbi':
species
The following object is masked from 'package:IRanges':
members
The following objects are masked from 'package:BiocGenerics':
counts, species
DAVID Result object
Result type: Gene List Report
ID
1 38926_at
2 38236_at
3 35367_at
4 1910_s_at
5 1391_s_at
6 38674_at
7 31576_at
8 606_at
9 34703_f_at
10 34233_i_at
11 40959_at
12 822_s_at
15 39469_s_at
16 41489_at
17 36713_at
18 37814_g_at
19 40350_at
20 39187_at
21 33979_at
22 36317_at
23 38691_s_at
24 36703_at
25 33516_at
26 34629_at
27 35069_at
28 1403_s_at
29 2090_i_at
30 1355_g_at
31 37172_at
32 38508_s_at
33 40058_s_at
34 936_s_at
35 31687_f_at
36 34539_at
37 36234_at
38 37953_s_at
39 33246_at
40 34546_at
41 1890_at
42 41703_r_at
43 33284_at
44 31525_s_at
45 34577_at
46 32680_at
47 34467_g_at
48 1372_at
49 38128_at
50 36328_at
51 32010_at
52 1331_s_at
53 40186_at
54 35915_at
55 31621_s_at
56 40294_at
57 37905_r_at
58 39511_at
59 31512_at
60 35595_at
61 35648_at
62 38201_at
63 40317_at
64 1974_s_at
65 39094_at
66 34623_at
67 33080_s_at
68 33530_at
69 38945_at
70 37954_at
71 37097_at
72 1419_g_at
73 37408_at
74 37096_at
75 1112_g_at
76 37061_at
77 34636_at
78 32413_at
79 35903_at
80 34606_s_at
81 39908_at
82 1855_at
83 33684_at
84 38948_at
85 1901_s_at
88 32073_at
89 32250_at
90 37166_at
91 32439_at
92 35956_s_at
93 35213_at
94 32717_at
95 37983_at
96 35373_at
97 38229_at
98 919_at
99 35896_at
100 35121_at
101 34249_at
102 34702_f_at
103 33685_at
104 35169_at
105 36436_at
106 36479_at
107 33293_at
110 37711_at
111 31987_at
112 1645_at
113 35439_at
114 36421_at
115 38646_s_at
116 34453_at
117 35038_at
118 34012_at
119 1575_at
120 36766_at
121 36696_at
122 32279_at
123 39198_s_at
124 35566_f_at
125 34529_at
126 40553_at
127 31715_at
128 34618_at
129 36378_at
130 38604_at
131 32418_at
132 32148_at
133 37898_r_at
134 38103_at
135 33922_at
136 41280_r_at
137 34436_at
138 37454_at
139 40790_at
140 33077_at
141 41113_at
142 33027_at
143 40089_at
144 38482_at
145 34972_s_at
146 32084_at
147 40735_at
150 33963_at
151 40271_at
152 37968_at
153 39698_at
154 32469_at
155 38816_at
156 1983_at
157 34720_at
158 1786_at
159 33371_s_at
Name
1 integrin, beta 5
2 glutamate receptor, ionotropic, N-methyl D-aspartate 2A
3 lectin, galactoside-binding, soluble, 3
4 B-cell CLL/lymphoma 2
5 cytochrome P450, family 4, subfamily A, polypeptide 11
6 kelch-like 9 (Drosophila)
7 mevalonate kinase
8 Rho family GTPase 2
9 HERV-H LTR-associating 1
10 natural killer-tumor recognition sequence
11 pleckstrin homology domain containing, family G (with RhoGef domain) member 3
12 CASP2 and RIPK1 domain containing adaptor with death domain
15 ATPase, aminophospholipid transporter-like, class I, type 8A, member 2
16 similar to transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila); transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)
17 tripartite motif-containing 58
18 DEAD (Asp-Glu-Ala-Asp) box polypeptide 51
19 ADAM metallopeptidase domain 23
20 runt-related transcription factor 2
21 ribonuclease, RNase A family, 3 (eosinophil cationic protein)
22 coronin, actin binding protein, 2A
23 surfactant protein C
24 chemokine (C-C motif) ligand 25
25 hemoglobin, delta
26 tumor protein p53 inducible protein 11
27 PRAME family member 2
28 chemokine (C-C motif) ligand 5
29 wingless-type MMTV integration site family, member 6
30 neurotrophic tyrosine kinase, receptor, type 2
31 carboxypeptidase B2 (plasma)
32 tenascin XB; tenascin XA pseudogene
33 PDZ and LIM domain 5
34 DNA segment on chromosome 4 (unique) 234 expressed sequence
35 hemoglobin, beta
36 olfactory receptor, family 7, subfamily E, member 35 pseudogene
37 similar to eukaryotic translation initiation factor 4A; small nucleolar RNA, H/ACA box 67; eukaryotic translation initiation factor 4A, isoform 1
38 amiloride-sensitive cation channel 2, neuronal
39 mitogen-activated protein kinase 13
40 defensin, alpha 4, corticostatin
41 growth differentiation factor 15
42 A kinase (PRKA) anchor protein 7
43 myeloperoxidase
44 hemoglobin, alpha 2; hemoglobin, alpha 1
45 melanoma antigen family A, 9; melanoma antigen family A, 9B
46 TRAF2 and NCK interacting kinase
47 5-hydroxytryptamine (serotonin) receptor 4
48 tumor necrosis factor, alpha-induced protein 6
49 N-acetyltransferase 8 (GCN5-related, putative); N-acetyltransferase 8B (GCN5-related, putative, gene/pseudogene)
50 sex hormone-binding globulin
51 chromosome 22 open reading frame 33
52 tumor necrosis factor receptor superfamily, member 25
53 dual specificity phosphatase 9
54 inhibin, beta C
55 elastin
56 ATP-binding cassette, sub-family B (MDR/TAP), member 9
57 guanine nucleotide binding protein-like 1
58 similar to Afadin (Protein AF-6); myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4
59 similar to hCG26659; immunoglobulin kappa constant; similar to Ig kappa chain V-I region HK102 precursor
60 CGRP receptor component
61 autism susceptibility candidate 2
62 branched chain aminotransferase 1, cytosolic
63 amiloride-sensitive cation channel 1, neuronal
64 tumor protein p53
65 bromodomain containing 4
66 defensin, alpha 5, Paneth cell-specific
67 RAP1 GTPase activating protein
68 carcinoembryonic antigen-related cell adhesion molecule 8
69 metal-regulatory transcription factor 1
70 annexin A8-like 2
71 solute carrier family 17 (sodium phosphate), member 1
72 nitric oxide synthase 2, inducible
73 mannose receptor, C type 2
74 elastase, neutrophil expressed
75 neural cell adhesion molecule 1
76 chitinase 1 (chitotriosidase)
77 arachidonate 15-lipoxygenase
78 ENSG00000178672
79 oligodendrocyte myelin glycoprotein
80 activating transcription factor 7
81 TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa
82 fibroblast growth factor 3 (murine mammary tumor virus integration site (v-int-2) oncogene homolog)
83 wingless-type MMTV integration site family, member 2B
84 protein phosphatase 1, regulatory (inhibitor) subunit 3D
85 v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)
88 lysine (K)-specific demethylase 4A
89 complement factor H
90 3-hydroxyanthranilate 3,4-dioxygenase
91 ATPase, H+/K+ exchanging, beta polypeptide
92 pregnancy specific beta-1-glycoprotein 7; pregnancy specific beta-1-glycoprotein 8; pregnancy specific beta-1-glycoprotein 4
93 WW domain binding protein 4 (formin binding protein 21)
94 neuralized homolog (Drosophila)
95 angiotensin II receptor, type 1
96 phosphoinositide-3-kinase, regulatory subunit 1 (alpha)
97 cytochrome P450, family 3, subfamily A, polypeptide 5
98 guanine nucleotide binding protein (G protein) alpha 12
99 POM121 membrane glycoprotein-like 9 (rat) pseudogene
100 solute carrier family 6 (neurotransmitter transporter, taurine), member 6
101 epilepsy, progressive myoclonus type 2A, Lafora disease (laforin)
102 TPTE pseudogene
103 ATPase, class I, type 8B, member 3
104 collagen, type XVI, alpha 1
105 leukocyte cell-derived chemotaxin 2
106 growth arrest-specific 8
107 Fas apoptotic inhibitory molecule 2
110 myocyte enhancer factor 2C
111 kin of IRRE like (Drosophila)
112 KiSS-1 metastasis-suppressor
113 splicing factor 1
114 cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)
115 regenerating islet-derived 1 alpha; regenerating islet-derived 1 pseudogene
116 cytochrome P450, family 2, subfamily B, polypeptide 7 pseudogene 1
117 myosin binding protein C, cardiac
118 keratin 34
119 ATP-binding cassette, sub-family B (MDR/TAP), member 1
120 ribonuclease, RNase A family, 2 (liver, eosinophil-derived neurotoxin)
121 phosphatidylinositol glycan anchor biosynthesis, class C
122 glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)
123 tetratricopeptide repeat domain 15
124 immunoglobulin heavy constant gamma 1 (G1m marker); immunoglobulin heavy constant mu; immunoglobulin heavy variable 3-7; immunoglobulin heavy constant gamma 3 (G3m marker); immunoglobulin heavy variable 3-11 (gene/pseudogene); immunoglobulin heavy variable 4-31; immunoglobulin heavy locus
125 hypothetical protein LOC729678
126 hypothetical LOC729400; hypothetical LOC728401; similar to Putative POM121-like protein 1-like
127 testis expressed 28; testis expressed 28 pseudogene 1; testis expressed 28 pseudogene 2
128 Indian hedgehog homolog (Drosophila)
129 uroplakin 1A
130 neuropeptide Y
131 phosphodiesterase 1C, calmodulin-dependent 70kDa
132 FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)
133 trefoil factor 3 (intestinal)
134 GRB10 interacting GYF protein 2
135 PR domain containing 2, with ZNF domain
136 mitogen-activated protein kinase 8 interacting protein 1
137 solute carrier family 17 (sodium phosphate), member 3
138 chemokine (C-C motif) ligand 13
139 basic helix-loop-helix family, member e40
140 sidekick homolog 1, cell adhesion molecule (chicken); hypothetical LOC730351
141 zinc finger protein 500
142 ArfGAP with GTPase domain, ankyrin repeat and PH domain 4; ArfGAP with GTPase domain, ankyrin repeat and PH domain 6
143 Williams Beuren syndrome chromosome region 22
144 claudin 7
145 dynein, axonemal, heavy chain 17
146 solute carrier family 22 (organic cation/carnitine transporter), member 5
147 histidine ammonia-lyase
150 azurocidin 1
151 nucleoporin 93kDa
152 natural cytotoxicity triggering receptor 3
153 HOP homeobox
154 carcinoembryonic antigen-related cell adhesion molecule 3
155 transforming, acidic coiled-coil containing protein 2
156 cyclin D2
157 nuclear factor I/B
158 c-mer proto-oncogene tyrosine kinase
159 RAB31, member RAS oncogene family
Species
1 Homo sapiens
2 Homo sapiens
3 Homo sapiens
4 Homo sapiens
5 Homo sapiens
6 Homo sapiens
7 Homo sapiens
8 Homo sapiens
9 Homo sapiens
10 Homo sapiens
11 Homo sapiens
12 Homo sapiens
15 Homo sapiens
16 Homo sapiens
17 Homo sapiens
18 Homo sapiens
19 Homo sapiens
20 Homo sapiens
21 Homo sapiens
22 Homo sapiens
23 Homo sapiens
24 Homo sapiens
25 Homo sapiens
26 Homo sapiens
27 Homo sapiens
28 Homo sapiens
29 Homo sapiens
30 Homo sapiens
31 Homo sapiens
32 Homo sapiens
33 Homo sapiens
34 Homo sapiens
35 Homo sapiens
36 Homo sapiens
37 Homo sapiens
38 Homo sapiens
39 Homo sapiens
40 Homo sapiens
41 Homo sapiens
42 Homo sapiens
43 Homo sapiens
44 Homo sapiens
45 Homo sapiens
46 Homo sapiens
47 Homo sapiens
48 Homo sapiens
49 Homo sapiens
50 Homo sapiens
51 Homo sapiens
52 Homo sapiens
53 Homo sapiens
54 Homo sapiens
55 Homo sapiens
56 Homo sapiens
57 Homo sapiens
58 Homo sapiens
59 Homo sapiens
60 Homo sapiens
61 Homo sapiens
62 Homo sapiens
63 Homo sapiens
64 Homo sapiens
65 Homo sapiens
66 Homo sapiens
67 Homo sapiens
68 Homo sapiens
69 Homo sapiens
70 Homo sapiens
71 Homo sapiens
72 Homo sapiens
73 Homo sapiens
74 Homo sapiens
75 Homo sapiens
76 Homo sapiens
77 Homo sapiens
78 Homo sapiens
79 Homo sapiens
80 Homo sapiens
81 Homo sapiens
82 Homo sapiens
83 Homo sapiens
84 Homo sapiens
85 Homo sapiens
88 Homo sapiens
89 Homo sapiens
90 Homo sapiens
91 Homo sapiens
92 Homo sapiens
93 Homo sapiens
94 Homo sapiens
95 Homo sapiens
96 Homo sapiens
97 Homo sapiens
98 Homo sapiens
99 Homo sapiens
100 Homo sapiens
101 Homo sapiens
102 Homo sapiens
103 Homo sapiens
104 Homo sapiens
105 Homo sapiens
106 Homo sapiens
107 Homo sapiens
110 Homo sapiens
111 Homo sapiens
112 Homo sapiens
113 Homo sapiens
114 Homo sapiens
115 Homo sapiens
116 Homo sapiens
117 Homo sapiens
118 Homo sapiens
119 Homo sapiens
120 Homo sapiens
121 Homo sapiens
122 Homo sapiens
123 Homo sapiens
124 Homo sapiens
125 Homo sapiens
126 Homo sapiens
127 Homo sapiens
128 Homo sapiens
129 Homo sapiens
130 Homo sapiens
131 Homo sapiens
132 Homo sapiens
133 Homo sapiens
134 Homo sapiens
135 Homo sapiens
136 Homo sapiens
137 Homo sapiens
138 Homo sapiens
139 Homo sapiens
140 Homo sapiens
141 Homo sapiens
142 Homo sapiens
143 Homo sapiens
144 Homo sapiens
145 Homo sapiens
146 Homo sapiens
147 Homo sapiens
150 Homo sapiens
151 Homo sapiens
152 Homo sapiens
153 Homo sapiens
154 Homo sapiens
155 Homo sapiens
156 Homo sapiens
157 Homo sapiens
158 Homo sapiens
159 Homo sapiens
RDAVIDWebService documentation built on Nov. 8, 2020, 8:05 p.m.
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Description Type Extends Slots Methods Author(s) References See Also Examples
Description
This class represents the output of "Show Genes Result" of DAVID. It is an heir of DAVIDResult in the conceptual way, and also a data.frame with additional features, such as identifying the unique and duplicate ids, searching for genes with a given id, etc.
Type
This class is a "Concrete" one.
Extends
-
DAVIDResultin the conceptual way. -
data.framein order to extend the basic features.
Slots
none additional to the ones inherited from DAVIDResult and data.frame classes.
Methods
validsignature(object="DAVIDGenes"): logical which checks for data.frame name (ID, Name) presence.DAVIDGenessignature(object="character"): constructor with the name of the .tab file report to load.DAVIDGenessignature(object="data.frame"): data.frame already loaded to use when constructing the object.idssignature(object="DAVIDGenes"): character vector with gene submitted ids.
Author(s)
Cristobal Fresno and Elmer A Fernandez
References
The Database for Annotation, Visualization and Integrated Discovery (david.abcc.ncifcrf.gov)
Huang, D. W.; Sherman, B. T.; Tan, Q.; Kir, J.; Liu, D.; Bryant, D.; Guo, Y.; Stephens, R.; Baseler, M. W.; Lane, H. C. & Lempicki, R. A. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res, Laboratory of Immunopathogenesis and Bioinformatics, SAIC-Frederick, Inc., National Cancer Institute at Frederick, MD 21702, USA., 2007, 35, W169-W175
See Also
Other DAVIDGenes:
DAVIDFunctionalAnnotationChart,
DAVIDFunctionalAnnotationChart,
DAVIDFunctionalAnnotationChart,
DAVIDFunctionalAnnotationTable,
DAVIDFunctionalAnnotationTable,
DAVIDFunctionalAnnotationTable,
DAVIDGODag, DAVIDGODag,
DAVIDGeneCluster,
DAVIDGeneCluster, DAVIDGenes,
DAVIDGenes, DAVIDGenes,
DAVIDTermCluster,
DAVIDTermCluster, as,
as, as, genes,
genes, genes,
genes, ids,
ids, ids, ids,
ids, initialize,
initialize, initialize,
initialize, initialize,
initialize, initialize
Examples
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 | {
##Load Show Gene List file report for the input demo file 1, using data
##function. Then, create a DAVIDGenes object using the loaded data.frame
##geneList1. In addition, the user can use the file name of the downloaded
##file report.
data(geneList1)
davidGenes1<-DAVIDGenes(geneList1)
##Now we can inspect davidGenes1 as it was an common data.frame
head(davidGenes1)
##Additional getters for this object are also available, to obtain the
##different columns: ids, genes and species.
ids(davidGenes1)
genes(davidGenes1)
species(davidGenes1)
##Or even look up for a particular gene id, which will return only the
##matched ones.
genes(davidGenes1, ids=c("38926_at", "35367_at", "no match"))
##Obtain the genes with duplicate manufacturer ids or just the genes that
##do not have duplicate ids (uniqueIds).
duplicateIds(davidGenes1)
uniqueIds(davidGenes1)
}
|
Example output
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: GOstats
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: Category
Loading required package: stats4
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Attaching package: 'GOstats'
The following object is masked from 'package:AnnotationDbi':
makeGOGraph
Loading required package: ggplot2
Attaching package: 'RDAVIDWebService'
The following object is masked from 'package:AnnotationDbi':
species
The following object is masked from 'package:IRanges':
members
The following objects are masked from 'package:BiocGenerics':
counts, species
DAVID Result object
Result type: Gene List Report
ID
1 38926_at
2 38236_at
3 35367_at
4 1910_s_at
5 1391_s_at
6 38674_at
7 31576_at
8 606_at
9 34703_f_at
10 34233_i_at
11 40959_at
12 822_s_at
15 39469_s_at
16 41489_at
17 36713_at
18 37814_g_at
19 40350_at
20 39187_at
21 33979_at
22 36317_at
23 38691_s_at
24 36703_at
25 33516_at
26 34629_at
27 35069_at
28 1403_s_at
29 2090_i_at
30 1355_g_at
31 37172_at
32 38508_s_at
33 40058_s_at
34 936_s_at
35 31687_f_at
36 34539_at
37 36234_at
38 37953_s_at
39 33246_at
40 34546_at
41 1890_at
42 41703_r_at
43 33284_at
44 31525_s_at
45 34577_at
46 32680_at
47 34467_g_at
48 1372_at
49 38128_at
50 36328_at
51 32010_at
52 1331_s_at
53 40186_at
54 35915_at
55 31621_s_at
56 40294_at
57 37905_r_at
58 39511_at
59 31512_at
60 35595_at
61 35648_at
62 38201_at
63 40317_at
64 1974_s_at
65 39094_at
66 34623_at
67 33080_s_at
68 33530_at
69 38945_at
70 37954_at
71 37097_at
72 1419_g_at
73 37408_at
74 37096_at
75 1112_g_at
76 37061_at
77 34636_at
78 32413_at
79 35903_at
80 34606_s_at
81 39908_at
82 1855_at
83 33684_at
84 38948_at
85 1901_s_at
88 32073_at
89 32250_at
90 37166_at
91 32439_at
92 35956_s_at
93 35213_at
94 32717_at
95 37983_at
96 35373_at
97 38229_at
98 919_at
99 35896_at
100 35121_at
101 34249_at
102 34702_f_at
103 33685_at
104 35169_at
105 36436_at
106 36479_at
107 33293_at
110 37711_at
111 31987_at
112 1645_at
113 35439_at
114 36421_at
115 38646_s_at
116 34453_at
117 35038_at
118 34012_at
119 1575_at
120 36766_at
121 36696_at
122 32279_at
123 39198_s_at
124 35566_f_at
125 34529_at
126 40553_at
127 31715_at
128 34618_at
129 36378_at
130 38604_at
131 32418_at
132 32148_at
133 37898_r_at
134 38103_at
135 33922_at
136 41280_r_at
137 34436_at
138 37454_at
139 40790_at
140 33077_at
141 41113_at
142 33027_at
143 40089_at
144 38482_at
145 34972_s_at
146 32084_at
147 40735_at
150 33963_at
151 40271_at
152 37968_at
153 39698_at
154 32469_at
155 38816_at
156 1983_at
157 34720_at
158 1786_at
159 33371_s_at
Name
1 integrin, beta 5
2 glutamate receptor, ionotropic, N-methyl D-aspartate 2A
3 lectin, galactoside-binding, soluble, 3
4 B-cell CLL/lymphoma 2
5 cytochrome P450, family 4, subfamily A, polypeptide 11
6 kelch-like 9 (Drosophila)
7 mevalonate kinase
8 Rho family GTPase 2
9 HERV-H LTR-associating 1
10 natural killer-tumor recognition sequence
11 pleckstrin homology domain containing, family G (with RhoGef domain) member 3
12 CASP2 and RIPK1 domain containing adaptor with death domain
15 ATPase, aminophospholipid transporter-like, class I, type 8A, member 2
16 similar to transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila); transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)
17 tripartite motif-containing 58
18 DEAD (Asp-Glu-Ala-Asp) box polypeptide 51
19 ADAM metallopeptidase domain 23
20 runt-related transcription factor 2
21 ribonuclease, RNase A family, 3 (eosinophil cationic protein)
22 coronin, actin binding protein, 2A
23 surfactant protein C
24 chemokine (C-C motif) ligand 25
25 hemoglobin, delta
26 tumor protein p53 inducible protein 11
27 PRAME family member 2
28 chemokine (C-C motif) ligand 5
29 wingless-type MMTV integration site family, member 6
30 neurotrophic tyrosine kinase, receptor, type 2
31 carboxypeptidase B2 (plasma)
32 tenascin XB; tenascin XA pseudogene
33 PDZ and LIM domain 5
34 DNA segment on chromosome 4 (unique) 234 expressed sequence
35 hemoglobin, beta
36 olfactory receptor, family 7, subfamily E, member 35 pseudogene
37 similar to eukaryotic translation initiation factor 4A; small nucleolar RNA, H/ACA box 67; eukaryotic translation initiation factor 4A, isoform 1
38 amiloride-sensitive cation channel 2, neuronal
39 mitogen-activated protein kinase 13
40 defensin, alpha 4, corticostatin
41 growth differentiation factor 15
42 A kinase (PRKA) anchor protein 7
43 myeloperoxidase
44 hemoglobin, alpha 2; hemoglobin, alpha 1
45 melanoma antigen family A, 9; melanoma antigen family A, 9B
46 TRAF2 and NCK interacting kinase
47 5-hydroxytryptamine (serotonin) receptor 4
48 tumor necrosis factor, alpha-induced protein 6
49 N-acetyltransferase 8 (GCN5-related, putative); N-acetyltransferase 8B (GCN5-related, putative, gene/pseudogene)
50 sex hormone-binding globulin
51 chromosome 22 open reading frame 33
52 tumor necrosis factor receptor superfamily, member 25
53 dual specificity phosphatase 9
54 inhibin, beta C
55 elastin
56 ATP-binding cassette, sub-family B (MDR/TAP), member 9
57 guanine nucleotide binding protein-like 1
58 similar to Afadin (Protein AF-6); myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4
59 similar to hCG26659; immunoglobulin kappa constant; similar to Ig kappa chain V-I region HK102 precursor
60 CGRP receptor component
61 autism susceptibility candidate 2
62 branched chain aminotransferase 1, cytosolic
63 amiloride-sensitive cation channel 1, neuronal
64 tumor protein p53
65 bromodomain containing 4
66 defensin, alpha 5, Paneth cell-specific
67 RAP1 GTPase activating protein
68 carcinoembryonic antigen-related cell adhesion molecule 8
69 metal-regulatory transcription factor 1
70 annexin A8-like 2
71 solute carrier family 17 (sodium phosphate), member 1
72 nitric oxide synthase 2, inducible
73 mannose receptor, C type 2
74 elastase, neutrophil expressed
75 neural cell adhesion molecule 1
76 chitinase 1 (chitotriosidase)
77 arachidonate 15-lipoxygenase
78 ENSG00000178672
79 oligodendrocyte myelin glycoprotein
80 activating transcription factor 7
81 TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa
82 fibroblast growth factor 3 (murine mammary tumor virus integration site (v-int-2) oncogene homolog)
83 wingless-type MMTV integration site family, member 2B
84 protein phosphatase 1, regulatory (inhibitor) subunit 3D
85 v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)
88 lysine (K)-specific demethylase 4A
89 complement factor H
90 3-hydroxyanthranilate 3,4-dioxygenase
91 ATPase, H+/K+ exchanging, beta polypeptide
92 pregnancy specific beta-1-glycoprotein 7; pregnancy specific beta-1-glycoprotein 8; pregnancy specific beta-1-glycoprotein 4
93 WW domain binding protein 4 (formin binding protein 21)
94 neuralized homolog (Drosophila)
95 angiotensin II receptor, type 1
96 phosphoinositide-3-kinase, regulatory subunit 1 (alpha)
97 cytochrome P450, family 3, subfamily A, polypeptide 5
98 guanine nucleotide binding protein (G protein) alpha 12
99 POM121 membrane glycoprotein-like 9 (rat) pseudogene
100 solute carrier family 6 (neurotransmitter transporter, taurine), member 6
101 epilepsy, progressive myoclonus type 2A, Lafora disease (laforin)
102 TPTE pseudogene
103 ATPase, class I, type 8B, member 3
104 collagen, type XVI, alpha 1
105 leukocyte cell-derived chemotaxin 2
106 growth arrest-specific 8
107 Fas apoptotic inhibitory molecule 2
110 myocyte enhancer factor 2C
111 kin of IRRE like (Drosophila)
112 KiSS-1 metastasis-suppressor
113 splicing factor 1
114 cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)
115 regenerating islet-derived 1 alpha; regenerating islet-derived 1 pseudogene
116 cytochrome P450, family 2, subfamily B, polypeptide 7 pseudogene 1
117 myosin binding protein C, cardiac
118 keratin 34
119 ATP-binding cassette, sub-family B (MDR/TAP), member 1
120 ribonuclease, RNase A family, 2 (liver, eosinophil-derived neurotoxin)
121 phosphatidylinositol glycan anchor biosynthesis, class C
122 glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)
123 tetratricopeptide repeat domain 15
124 immunoglobulin heavy constant gamma 1 (G1m marker); immunoglobulin heavy constant mu; immunoglobulin heavy variable 3-7; immunoglobulin heavy constant gamma 3 (G3m marker); immunoglobulin heavy variable 3-11 (gene/pseudogene); immunoglobulin heavy variable 4-31; immunoglobulin heavy locus
125 hypothetical protein LOC729678
126 hypothetical LOC729400; hypothetical LOC728401; similar to Putative POM121-like protein 1-like
127 testis expressed 28; testis expressed 28 pseudogene 1; testis expressed 28 pseudogene 2
128 Indian hedgehog homolog (Drosophila)
129 uroplakin 1A
130 neuropeptide Y
131 phosphodiesterase 1C, calmodulin-dependent 70kDa
132 FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)
133 trefoil factor 3 (intestinal)
134 GRB10 interacting GYF protein 2
135 PR domain containing 2, with ZNF domain
136 mitogen-activated protein kinase 8 interacting protein 1
137 solute carrier family 17 (sodium phosphate), member 3
138 chemokine (C-C motif) ligand 13
139 basic helix-loop-helix family, member e40
140 sidekick homolog 1, cell adhesion molecule (chicken); hypothetical LOC730351
141 zinc finger protein 500
142 ArfGAP with GTPase domain, ankyrin repeat and PH domain 4; ArfGAP with GTPase domain, ankyrin repeat and PH domain 6
143 Williams Beuren syndrome chromosome region 22
144 claudin 7
145 dynein, axonemal, heavy chain 17
146 solute carrier family 22 (organic cation/carnitine transporter), member 5
147 histidine ammonia-lyase
150 azurocidin 1
151 nucleoporin 93kDa
152 natural cytotoxicity triggering receptor 3
153 HOP homeobox
154 carcinoembryonic antigen-related cell adhesion molecule 3
155 transforming, acidic coiled-coil containing protein 2
156 cyclin D2
157 nuclear factor I/B
158 c-mer proto-oncogene tyrosine kinase
159 RAB31, member RAS oncogene family
Species
1 Homo sapiens
2 Homo sapiens
3 Homo sapiens
4 Homo sapiens
5 Homo sapiens
6 Homo sapiens
7 Homo sapiens
8 Homo sapiens
9 Homo sapiens
10 Homo sapiens
11 Homo sapiens
12 Homo sapiens
15 Homo sapiens
16 Homo sapiens
17 Homo sapiens
18 Homo sapiens
19 Homo sapiens
20 Homo sapiens
21 Homo sapiens
22 Homo sapiens
23 Homo sapiens
24 Homo sapiens
25 Homo sapiens
26 Homo sapiens
27 Homo sapiens
28 Homo sapiens
29 Homo sapiens
30 Homo sapiens
31 Homo sapiens
32 Homo sapiens
33 Homo sapiens
34 Homo sapiens
35 Homo sapiens
36 Homo sapiens
37 Homo sapiens
38 Homo sapiens
39 Homo sapiens
40 Homo sapiens
41 Homo sapiens
42 Homo sapiens
43 Homo sapiens
44 Homo sapiens
45 Homo sapiens
46 Homo sapiens
47 Homo sapiens
48 Homo sapiens
49 Homo sapiens
50 Homo sapiens
51 Homo sapiens
52 Homo sapiens
53 Homo sapiens
54 Homo sapiens
55 Homo sapiens
56 Homo sapiens
57 Homo sapiens
58 Homo sapiens
59 Homo sapiens
60 Homo sapiens
61 Homo sapiens
62 Homo sapiens
63 Homo sapiens
64 Homo sapiens
65 Homo sapiens
66 Homo sapiens
67 Homo sapiens
68 Homo sapiens
69 Homo sapiens
70 Homo sapiens
71 Homo sapiens
72 Homo sapiens
73 Homo sapiens
74 Homo sapiens
75 Homo sapiens
76 Homo sapiens
77 Homo sapiens
78 Homo sapiens
79 Homo sapiens
80 Homo sapiens
81 Homo sapiens
82 Homo sapiens
83 Homo sapiens
84 Homo sapiens
85 Homo sapiens
88 Homo sapiens
89 Homo sapiens
90 Homo sapiens
91 Homo sapiens
92 Homo sapiens
93 Homo sapiens
94 Homo sapiens
95 Homo sapiens
96 Homo sapiens
97 Homo sapiens
98 Homo sapiens
99 Homo sapiens
100 Homo sapiens
101 Homo sapiens
102 Homo sapiens
103 Homo sapiens
104 Homo sapiens
105 Homo sapiens
106 Homo sapiens
107 Homo sapiens
110 Homo sapiens
111 Homo sapiens
112 Homo sapiens
113 Homo sapiens
114 Homo sapiens
115 Homo sapiens
116 Homo sapiens
117 Homo sapiens
118 Homo sapiens
119 Homo sapiens
120 Homo sapiens
121 Homo sapiens
122 Homo sapiens
123 Homo sapiens
124 Homo sapiens
125 Homo sapiens
126 Homo sapiens
127 Homo sapiens
128 Homo sapiens
129 Homo sapiens
130 Homo sapiens
131 Homo sapiens
132 Homo sapiens
133 Homo sapiens
134 Homo sapiens
135 Homo sapiens
136 Homo sapiens
137 Homo sapiens
138 Homo sapiens
139 Homo sapiens
140 Homo sapiens
141 Homo sapiens
142 Homo sapiens
143 Homo sapiens
144 Homo sapiens
145 Homo sapiens
146 Homo sapiens
147 Homo sapiens
150 Homo sapiens
151 Homo sapiens
152 Homo sapiens
153 Homo sapiens
154 Homo sapiens
155 Homo sapiens
156 Homo sapiens
157 Homo sapiens
158 Homo sapiens
159 Homo sapiens
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