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Coexpression cluster:C4438: Difference between revisions

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|full_id=C4438_Mast_placenta_chorionic_mesenchymal_chronic_testicular_mesothelioma
|full_id=C4438_Mast_placenta_chorionic_mesenchymal_chronic_testicular_mesothelioma
|id=C4438
|id=C4438
|ontology_enrichment_celltype=CL:0000037!9.94e-29!172;CL:0000566!9.94e-29!172;CL:0002032!3.67e-28!165;CL:0000837!3.67e-28!165;CL:0000763!8.22e-24!112;CL:0000049!8.22e-24!112;CL:0000988!1.44e-23!182;CL:0002031!7.03e-23!124;CL:0000557!4.77e-21!71;CL:0000738!9.71e-21!140;CL:0002087!2.33e-20!119;CL:0000839!3.54e-19!70;CL:0002009!9.89e-18!65;CL:0002194!1.04e-16!63;CL:0000576!1.04e-16!63;CL:0000040!1.04e-16!63;CL:0000559!1.04e-16!63;CL:0000766!3.37e-15!76;CL:0000860!6.88e-13!45;CL:0002057!1.72e-11!42;CL:0000063!9.30e-07!578
|ontology_enrichment_celltype=CL:0000037!5.56e-26!168;CL:0000566!5.56e-26!168;CL:0002032!4.51e-25!161;CL:0000837!4.51e-25!161;CL:0000988!3.43e-21!177;CL:0000763!4.82e-21!108;CL:0000049!4.82e-21!108;CL:0002031!4.85e-20!120;CL:0000738!2.15e-18!136;CL:0000557!2.47e-18!67;CL:0002087!7.59e-18!115;CL:0000839!1.57e-16!66;CL:0002009!3.03e-15!61;CL:0002194!3.10e-14!59;CL:0000576!3.10e-14!59;CL:0000040!3.10e-14!59;CL:0000559!3.10e-14!59;CL:0000766!5.90e-13!72;CL:0000860!2.27e-11!42;CL:0002057!2.27e-11!42;CL:0000473!2.87e-11!48;CL:0000234!2.87e-11!48
|ontology_enrichment_disease=DOID:162!2.98e-11!235;DOID:14566!3.97e-11!239;DOID:2531!3.60e-09!51;DOID:0060083!3.60e-09!51;DOID:8692!6.85e-09!31;DOID:1240!1.62e-08!39;DOID:305!8.24e-08!106
|ontology_enrichment_disease=DOID:162!3.29e-12!235;DOID:14566!8.11e-12!239;DOID:2531!6.21e-09!51;DOID:0060083!6.21e-09!51;DOID:305!6.62e-09!106;DOID:8692!1.31e-08!31;DOID:1240!3.74e-08!39
|ontology_enrichment_uberon=UBERON:0002371!3.73e-16!80;UBERON:0002405!2.07e-14!115;UBERON:0002193!2.69e-14!112;UBERON:0001474!6.28e-14!86;UBERON:0002390!3.28e-13!102;UBERON:0003061!3.28e-13!102;UBERON:0004765!5.59e-09!101;UBERON:0001434!5.59e-09!101
|ontology_enrichment_uberon=UBERON:0002405!6.51e-16!93;UBERON:0002371!8.01e-14!76;UBERON:0002193!3.05e-12!108;UBERON:0001474!6.11e-12!82;UBERON:0002390!2.02e-11!98;UBERON:0003061!2.02e-11!98;UBERON:0004765!9.68e-10!90
|tf_chipseq_enrich=BATF#10538;3:24.3578017923036:6.91705216281876e-05:0.00110173861649021!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280786439955995!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323760412127173!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00900675158730585!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00243836428684486!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00388965522609599!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438410294574268!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392856994767158!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123272924093493!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000759355613631687!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445751451105074!JUNB#3726;3:30.6106326598211:3.4847716247536e-05:0.000681802292464671!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015737729469737!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187187209350311!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00722205317963704!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270481799574124!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00884688386377488!RXRA#6256;2:13.3830780927555:0.00719643442946573:0.0298379616252718!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.00072159581538009!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00390210858497757
|tf_chipseq_enrich=BATF#10538;3:24.3578017923036:6.91705216281876e-05:0.00110173861649021!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280786439955995!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323760412127173!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00900675158730585!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00243836428684486!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00388965522609599!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438410294574268!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392856994767158!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123272924093493!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000759355613631687!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445751451105074!JUNB#3726;3:30.6106326598211:3.4847716247536e-05:0.000681802292464671!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015737729469737!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187187209350311!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00722205317963704!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270481799574124!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00884688386377488!RXRA#6256;2:13.3830780927555:0.00719643442946573:0.0298379616252718!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.00072159581538009!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00390210858497757
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}}
}}

Revision as of 15:57, 19 October 2012


Full id: C4438_Mast_placenta_chorionic_mesenchymal_chronic_testicular_mesothelioma



Phase1 CAGE Peaks

Hg19::chr4:87857474..87857489,+p7@AFF1
Hg19::chr4:87857491..87857519,+p10@AFF1
Hg19::chr4:87857538..87857549,+p19@AFF1


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>


Uber Anatomy
Ontology termp-valuen
immune system6.51e-1693
bone marrow8.01e-1476
hemolymphoid system3.05e-12108
bone element6.11e-1282
hematopoietic system2.02e-1198
blood island2.02e-1198
skeletal element9.68e-1090
Disease
Ontology termp-valuen
cancer3.29e-12235
disease of cellular proliferation8.11e-12239
hematologic cancer6.21e-0951
immune system cancer6.21e-0951
carcinoma6.62e-09106
myeloid leukemia1.31e-0831
leukemia3.74e-0839


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
BATF#10538324.35780179230366.91705216281876e-050.00110173861649021
CTCF#1066435.360256373075030.0064925092527670.0280786439955995
E2F6#187635.017155731697390.00791769806886330.0323760412127173
FOS#235338.99795530889440.001372499272417130.00900675158730585
FOSL2#2355316.93020060456170.0002060162053171620.00243836428684486
GATA1#2623313.56030814380040.0004009615963782630.00388965522609599
GATA2#2624312.7449317335540.0004829527704283790.00438410294574268
HDAC2#3066313.41562023662630.0004140761399857210.00392856994767158
HNF4A#3172323.13229036295378.07584663437677e-050.00123272924093493
HNF4G#3174328.75342252644684.20470658818262e-050.000759355613631687
JUN#3725312.51282919233630.0005103313992726250.00445751451105074
JUNB#3726330.61063265982113.4847716247536e-050.000681802292464671
JUND#372736.994663941871030.002921845042734990.015737729469737
MAX#414936.452555509007120.003721913834265510.0187187209350311
MXI1#460139.96157162875930.001011470541259020.00722205317963704
NFKB1#479035.488063424193840.006049381815655430.0270481799574124
POU2F2#545239.106124057742520.001324165192682130.00884688386377488
RXRA#6256213.38307809275550.007196434429465730.0298379616252718
TAL1#6886329.86861667744023.75103522793067e-050.00072159581538009
ZNF143#7702313.50087655222790.0004062804962997170.00390210858497757



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.