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Coexpression cluster:C4235: Difference between revisions

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|ontology_enrichment_disease=DOID:305!3.07e-35!106;DOID:0050687!7.39e-29!143;DOID:299!1.09e-14!25;DOID:162!1.93e-13!235;DOID:14566!2.29e-13!239;DOID:1749!1.56e-08!14;DOID:7!4.17e-07!39
|ontology_enrichment_disease=DOID:305!3.07e-35!106;DOID:0050687!7.39e-29!143;DOID:299!1.09e-14!25;DOID:162!1.93e-13!235;DOID:14566!2.29e-13!239;DOID:1749!1.56e-08!14;DOID:7!4.17e-07!39
|ontology_enrichment_uberon=UBERON:0001007!1.65e-13!155;UBERON:0001555!1.65e-13!155;UBERON:0007026!1.65e-13!155;UBERON:0004119!2.67e-13!169;UBERON:0000925!2.67e-13!169;UBERON:0006595!2.67e-13!169;UBERON:0005177!1.11e-12!107;UBERON:0005911!6.00e-12!82;UBERON:0004921!7.51e-12!129;UBERON:0004185!7.51e-12!129;UBERON:0000466!1.21e-11!126;UBERON:0000464!7.11e-11!104;UBERON:0000062!1.64e-10!511;UBERON:0005153!1.17e-09!37;UBERON:0000481!1.94e-09!347;UBERON:0000064!3.25e-09!219;UBERON:0009569!4.30e-09!113;UBERON:0000489!5.71e-09!32;UBERON:0006554!6.70e-09!44;UBERON:0002113!1.15e-08!27;UBERON:0003918!1.15e-08!27;UBERON:0005095!1.15e-08!27;UBERON:0007687!1.15e-08!27;UBERON:0001008!1.90e-08!45;UBERON:0005172!2.47e-08!55;UBERON:0005173!2.47e-08!55;UBERON:0000077!2.73e-08!130;UBERON:0002048!5.02e-08!22;UBERON:0000117!5.02e-08!22;UBERON:0000171!5.02e-08!22;UBERON:0000170!5.02e-08!22;UBERON:0005597!5.02e-08!22;UBERON:0000118!5.02e-08!22;UBERON:0000058!5.49e-08!26;UBERON:0003064!5.75e-08!37;UBERON:0005409!5.86e-08!35;UBERON:0000080!3.27e-07!18;UBERON:0002120!3.27e-07!18;UBERON:0004875!3.27e-07!18;UBERON:0005721!3.27e-07!18;UBERON:0005754!3.27e-07!18;UBERON:0007297!3.27e-07!18;UBERON:0005157!5.24e-07!51;UBERON:0000160!7.51e-07!27;UBERON:0006555!8.34e-07!17;UBERON:0005103!8.34e-07!17;UBERON:0000083!8.34e-07!17;UBERON:0009201!8.34e-07!17;UBERON:0004819!8.34e-07!17;UBERON:0006553!8.34e-07!17;UBERON:0003074!8.34e-07!17;UBERON:0003060!8.34e-07!17
|ontology_enrichment_uberon=UBERON:0001007!1.65e-13!155;UBERON:0001555!1.65e-13!155;UBERON:0007026!1.65e-13!155;UBERON:0004119!2.67e-13!169;UBERON:0000925!2.67e-13!169;UBERON:0006595!2.67e-13!169;UBERON:0005177!1.11e-12!107;UBERON:0005911!6.00e-12!82;UBERON:0004921!7.51e-12!129;UBERON:0004185!7.51e-12!129;UBERON:0000466!1.21e-11!126;UBERON:0000464!7.11e-11!104;UBERON:0000062!1.64e-10!511;UBERON:0005153!1.17e-09!37;UBERON:0000481!1.94e-09!347;UBERON:0000064!3.25e-09!219;UBERON:0009569!4.30e-09!113;UBERON:0000489!5.71e-09!32;UBERON:0006554!6.70e-09!44;UBERON:0002113!1.15e-08!27;UBERON:0003918!1.15e-08!27;UBERON:0005095!1.15e-08!27;UBERON:0007687!1.15e-08!27;UBERON:0001008!1.90e-08!45;UBERON:0005172!2.47e-08!55;UBERON:0005173!2.47e-08!55;UBERON:0000077!2.73e-08!130;UBERON:0002048!5.02e-08!22;UBERON:0000117!5.02e-08!22;UBERON:0000171!5.02e-08!22;UBERON:0000170!5.02e-08!22;UBERON:0005597!5.02e-08!22;UBERON:0000118!5.02e-08!22;UBERON:0000058!5.49e-08!26;UBERON:0003064!5.75e-08!37;UBERON:0005409!5.86e-08!35;UBERON:0000080!3.27e-07!18;UBERON:0002120!3.27e-07!18;UBERON:0004875!3.27e-07!18;UBERON:0005721!3.27e-07!18;UBERON:0005754!3.27e-07!18;UBERON:0007297!3.27e-07!18;UBERON:0005157!5.24e-07!51;UBERON:0000160!7.51e-07!27;UBERON:0006555!8.34e-07!17;UBERON:0005103!8.34e-07!17;UBERON:0000083!8.34e-07!17;UBERON:0009201!8.34e-07!17;UBERON:0004819!8.34e-07!17;UBERON:0006553!8.34e-07!17;UBERON:0003074!8.34e-07!17;UBERON:0003060!8.34e-07!17
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}}
}}

Revision as of 12:36, 5 September 2012


Full id: C4235_nonsmall_endometrial_colon_small_tubular_argyrophil_Prostate



Phase1 CAGE Peaks

Hg19::chr2:47596330..47596380,+p2@EPCAM
Hg19::chr2:47596386..47596392,+p7@EPCAM
Hg19::chr2:47596394..47596400,+p6@EPCAM


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell7.73e-26254
endodermal cell9.67e-1159
endo-epithelial cell1.13e-0943
kidney cell4.48e-0718
kidney epithelial cell4.48e-0718
Uber Anatomy
Ontology termp-valuen
digestive system1.65e-13155
digestive tract1.65e-13155
primitive gut1.65e-13155
endoderm-derived structure2.67e-13169
endoderm2.67e-13169
presumptive endoderm2.67e-13169
trunk region element1.11e-12107
endo-epithelium6.00e-1282
subdivision of digestive tract7.51e-12129
endodermal part of digestive tract7.51e-12129
immaterial anatomical entity1.21e-11126
anatomical space7.11e-11104
organ1.64e-10511
epithelial bud1.17e-0937
multi-tissue structure1.94e-09347
organ part3.25e-09219
subdivision of trunk4.30e-09113
cavitated compound organ5.71e-0932
urinary system structure6.70e-0944
kidney1.15e-0827
kidney mesenchyme1.15e-0827
kidney rudiment1.15e-0827
kidney field1.15e-0827
renal system1.90e-0845
abdomen element2.47e-0855
abdominal segment element2.47e-0855
mixed endoderm/mesoderm-derived structure2.73e-08130
lung5.02e-0822
respiratory tube5.02e-0822
respiration organ5.02e-0822
pair of lungs5.02e-0822
lung primordium5.02e-0822
lung bud5.02e-0822
duct5.49e-0826
intermediate mesoderm5.75e-0837
gastrointestinal system5.86e-0835
mesonephros3.27e-0718
pronephros3.27e-0718
nephrogenic cord3.27e-0718
pronephric mesoderm3.27e-0718
rostral part of nephrogenic cord3.27e-0718
presumptive pronephric mesoderm3.27e-0718
epithelial fold5.24e-0751
intestine7.51e-0727
excretory tube8.34e-0717
mesonephric epithelium8.34e-0717
mesonephric tubule8.34e-0717
nephric duct8.34e-0717
kidney epithelium8.34e-0717
renal duct8.34e-0717
mesonephric duct8.34e-0717
pronephric duct8.34e-0717
Disease
Ontology termp-valuen
carcinoma3.07e-35106
cell type cancer7.39e-29143
adenocarcinoma1.09e-1425
cancer1.93e-13235
disease of cellular proliferation2.29e-13239
squamous cell carcinoma1.56e-0814
disease of anatomical entity4.17e-0739


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#467322.46317452600878.81932387510763e-050.00129839493401799
CCNT2#90536.336201576962630.003930750035764890.0190515872927998
E2F1#186934.907389214879320.008460985347239390.0326361666671715
E2F6#187635.017155731697390.00791769806886330.0323190990625347
EP300#203336.77394172622320.003216880500103790.0167866384805806
FOS#235338.99795530889440.001372499272417130.00899601176804146
FOSL1#8061339.7135797163731.59554825631833e-050.000371792646902343
FOSL2#2355316.93020060456170.0002060162053171620.00243587982193129
JUN#3725312.51282919233630.0005103313992726250.00445118598702469
JUND#372736.994663941871030.002921845042734990.0157134178382183
MYC#460935.22228187160940.007020843755740150.029527237990003
NANOG#79923329.24477848101273.99627955670032e-050.000739357733608902
RXRA#6256320.07461713913330.0001235730348432220.00165544435428313
SP1#666735.69838137814090.005403962701712170.0247146812315693
TAF7#6879311.43306940492390.0006690181981945830.00544383261404317
TCF12#6938310.63446490218640.0008313523990202070.00630358742567674
YY1#752834.911170749853860.008441455341808260.0330206058070757
ZNF263#1012738.221841637010680.001799043925565870.0109678564323259



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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