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Coexpression cluster:C4372: Difference between revisions

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|full_id=C4372_CD14_maxillary_smallcell_glioblastoma_Mammary_small_gastric
|full_id=C4372_CD14_maxillary_smallcell_glioblastoma_Mammary_small_gastric
|id=C4372
|id=C4372
|ontology_enrichment_celltype=CL:0000066!2.74e-18!254;CL:0000063!1.42e-14!578;CL:0000548!1.52e-14!679;CL:0000004!1.52e-14!679;CL:0000255!1.52e-14!679;CL:0000012!7.08e-14!682;CL:0000860!5.60e-09!45;CL:0000003!1.52e-08!722;CL:0000076!4.12e-08!62;CL:0002057!7.31e-08!42;CL:0000223!5.85e-07!59
|ontology_enrichment_celltype=CL:0000066!7.11e-19!253;CL:0000548!1.03e-14!679;CL:0000255!1.03e-14!679;CL:0000860!1.46e-08!42;CL:0002057!1.46e-08!42;CL:0000076!2.20e-08!63;CL:0000003!2.68e-08!722;CL:0000223!4.42e-07!58;CL:0002076!6.01e-07!42
|ontology_enrichment_disease=DOID:305!5.93e-18!106;DOID:0050687!2.06e-17!143;DOID:162!3.94e-16!235;DOID:14566!5.10e-16!239
|ontology_enrichment_disease=DOID:305!6.77e-18!106;DOID:0050687!5.81e-17!143;DOID:162!4.11e-16!235;DOID:14566!8.48e-16!239
|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.0012994940267951!BATF#10538;3:24.3578017923036:6.91705216281876e-05:0.00110123477261071!BCLAF1#9774;3:21.6526476101218:9.8473954032885e-05:0.00139432230005972!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115572938266413!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280658598447737!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326820344951673!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323633700682562!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464086495937243!EP300#2033;3:6.7739417262232:0.00321688050010379:0.016803430156564!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00900279182966792!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00243698340323016!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00583108710020466!GTF2B#2959;3:31.9438299343242:3.06634405746243e-05:0.000629166811428918!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00435209755626886!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392714293352422!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445527886053947!JUND#3727;3:6.99466394187103:0.00292184504273499:0.01573042808486!MAFF#23764;3:56.3153564899452:5.59409009993116e-06:0.000169149153429852!MAFK#7975;3:27.1007331378299:5.02195559325033e-05:0.000858690275382239!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187160170897422!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00722007872726068!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295546110844718!NFE2#4778;3:77.204260651629:2.17039522930409e-06:7.84067476144207e-05!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270400765009732!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00137151746001685!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00884405503348014!REST#5978;3:9.65002871612802:0.00111263624711459:0.00769961681767828!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165735767124583!SETDB1#9869;3:40.3200261780105:1.52461559299059e-05:0.000359677722874055!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277720014316145!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247450219486197!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00644568400640975!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00544680321182133!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.000721330083170412!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00630816718986278!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00616131690714602!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197621157042495!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190909880173987!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330577507384271!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243415809274312
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}}
}}

Revision as of 15:54, 19 October 2012


Full id: C4372_CD14_maxillary_smallcell_glioblastoma_Mammary_small_gastric



Phase1 CAGE Peaks

Hg19::chr4:139163398..139163413,-p4@SLC7A11
Hg19::chr4:139163421..139163430,-p5@SLC7A11
Hg19::chr4:139163521..139163536,-p2@SLC7A11


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><br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell7.11e-19253
animal cell1.03e-14679
eukaryotic cell1.03e-14679
classical monocyte1.46e-0842
CD14-positive, CD16-negative classical monocyte1.46e-0842
squamous epithelial cell2.20e-0863
native cell2.68e-08722
endodermal cell4.42e-0758
endo-epithelial cell6.01e-0742
Disease
Ontology termp-valuen
carcinoma6.77e-18106
cell type cancer5.81e-17143
cancer4.11e-16235
disease of cellular proliferation8.48e-16239


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-050.0012994940267951
BATF#10538324.35780179230366.91705216281876e-050.00110123477261071
BCLAF1#9774321.65264761012189.8473954032885e-050.00139432230005972
CEBPB#105137.971147625824820.001974187055288560.0115572938266413
CTCF#1066435.360256373075030.0064925092527670.0280658598447737
E2F1#186934.907389214879320.008460985347239390.0326820344951673
E2F6#187635.017155731697390.00791769806886330.0323633700682562
ELF1#199734.258097958807540.01295179875054610.0464086495937243
EP300#203336.77394172622320.003216880500103790.016803430156564
FOS#235338.99795530889440.001372499272417130.00900279182966792
FOSL2#2355316.93020060456170.0002060162053171620.00243698340323016
FOXA1#3169311.08141974938550.000734755275698670.00583108710020466
GTF2B#2959331.94382993432423.06634405746243e-050.000629166811428918
GTF2F1#2962312.73966087675770.0004835525047438590.00435209755626886
HDAC2#3066313.41562023662630.0004140761399857210.00392714293352422
JUN#3725312.51282919233630.0005103313992726250.00445527886053947
JUND#372736.994663941871030.002921845042734990.01573042808486
MAFF#23764356.31535648994525.59409009993116e-060.000169149153429852
MAFK#7975327.10073313782995.02195559325033e-050.000858690275382239
MAX#414936.452555509007120.003721913834265510.0187160170897422
MXI1#460139.96157162875930.001011470541259020.00722007872726068
MYC#460935.22228187160940.007020843755740150.0295546110844718
NFE2#4778377.2042606516292.17039522930409e-067.84067476144207e-05
NFKB1#479035.488063424193840.006049381815655430.0270400765009732
PBX3#5090321.91451268674419.49854535978121e-050.00137151746001685
POU2F2#545239.106124057742520.001324165192682130.00884405503348014
REST#597839.650028716128020.001112636247114590.00769961681767828
RXRA#6256320.07461713913330.0001235730348432220.00165735767124583
SETDB1#9869340.32002617801051.52461559299059e-050.000359677722874055
SIN3A#2594235.408884726815140.006318961977991520.0277720014316145
SP1#666735.69838137814090.005403962701712170.0247450219486197
STAT3#6774310.51946499715420.0008589184530415310.00644568400640975
TAF7#6879311.43306940492390.0006690181981945830.00544680321182133
TAL1#6886329.86861667744023.75103522793067e-050.000721330083170412
TCF12#6938310.63446490218640.0008313523990202070.00630816718986278
TCF7L2#6934310.77017656313730.0008003181298398380.00616131690714602
TRIM28#10155318.59052504526250.0001555969297255280.00197621157042495
USF1#739136.361499277207960.00388404057290560.0190909880173987
YY1#752834.911170749853860.008441455341808260.0330577507384271
ZEB1#6935316.88843201754390.0002075486917327580.00243415809274312



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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