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Coexpression cluster:C2058: Difference between revisions

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|full_id=C2058_Smooth_basal_mesenchymal_tubular_Renal_lung_Urothelial
|full_id=C2058_Smooth_basal_mesenchymal_tubular_Renal_lung_Urothelial
|id=C2058
|id=C2058
|ontology_enrichment_celltype=CL:0000220!2.02e-26!246;CL:0002321!3.37e-26!248;CL:0000548!5.84e-25!679;CL:0000004!5.84e-25!679;CL:0000255!5.84e-25!679;CL:0000012!5.77e-24!682;CL:0000055!1.49e-21!180;CL:0000222!6.70e-20!119;CL:0000144!4.31e-17!625;CL:0000066!4.91e-17!254;CL:0002371!2.29e-16!591;CL:0000359!3.31e-16!32;CL:0000680!1.03e-15!57;CL:0000056!1.03e-15!57;CL:0000355!1.03e-15!57;CL:0000187!1.20e-14!54;CL:0000192!1.82e-14!42;CL:0000514!1.82e-14!42;CL:0000183!5.37e-14!59;CL:0000393!6.97e-13!60;CL:0000211!6.97e-13!60;CL:0000003!4.42e-12!722;CL:0000057!1.32e-11!75;CL:0000063!3.38e-09!578;CL:0002076!9.15e-07!43
|ontology_enrichment_celltype=CL:0002321!7.93e-26!250;CL:0000548!2.21e-22!679;CL:0000255!2.21e-22!679;CL:0000222!4.59e-19!121;CL:0000359!9.11e-17!32;CL:0000680!2.84e-16!58;CL:0000056!2.84e-16!58;CL:0000355!2.84e-16!58;CL:0000187!2.69e-15!55;CL:0002371!3.03e-15!588;CL:0000192!4.68e-15!43;CL:0000514!4.68e-15!43;CL:0000066!6.65e-15!253;CL:0000183!2.48e-14!59;CL:0000393!4.07e-14!61;CL:0000211!4.07e-14!61;CL:0000057!1.07e-11!76;CL:0000003!1.85e-11!722;CL:0000055!3.44e-10!106
|ontology_enrichment_disease=DOID:2394!2.11e-08!14;DOID:120!8.57e-07!27;DOID:193!9.92e-07!29
|ontology_enrichment_disease=DOID:2394!2.97e-08!14
|ontology_enrichment_uberon=UBERON:0003914!2.20e-21!118;UBERON:0002100!4.96e-20!216;UBERON:0005256!6.78e-19!143;UBERON:0002049!1.06e-18!79;UBERON:0007798!1.06e-18!79;UBERON:0001637!2.73e-18!42;UBERON:0003509!2.73e-18!42;UBERON:0004572!2.73e-18!42;UBERON:0000490!1.01e-17!138;UBERON:0004872!1.47e-17!84;UBERON:0001981!2.24e-17!60;UBERON:0007500!2.24e-17!60;UBERON:0004537!2.24e-17!60;UBERON:0006965!2.24e-17!60;UBERON:0000486!4.27e-17!82;UBERON:0000914!9.69e-17!83;UBERON:0002329!9.69e-17!83;UBERON:0003077!9.69e-17!83;UBERON:0003059!9.69e-17!83;UBERON:0007282!9.69e-17!83;UBERON:0009618!9.69e-17!83;UBERON:0007285!9.69e-17!83;UBERON:0003104!1.54e-16!238;UBERON:0009142!1.54e-16!238;UBERON:0000926!1.64e-16!448;UBERON:0004120!1.64e-16!448;UBERON:0006603!1.64e-16!448;UBERON:0000055!1.78e-16!69;UBERON:0004573!8.33e-16!33;UBERON:0004571!8.33e-16!33;UBERON:0004290!4.59e-15!70;UBERON:0004535!3.99e-14!110;UBERON:0001009!1.98e-13!113;UBERON:0001134!2.25e-13!61;UBERON:0002036!2.25e-13!61;UBERON:0003082!2.25e-13!61;UBERON:0002385!7.33e-13!63;UBERON:0001015!7.33e-13!63;UBERON:0000383!7.33e-13!63;UBERON:0000467!4.98e-11!625;UBERON:0000480!8.42e-11!626;UBERON:0000468!1.19e-10!659;UBERON:0000947!2.94e-09!21;UBERON:0010191!2.94e-09!21;UBERON:0003102!5.28e-08!95;UBERON:0000475!2.60e-07!365;UBERON:0000481!5.80e-07!347;UBERON:0002199!8.94e-07!45;UBERON:0002416!8.94e-07!45;UBERON:0003886!9.20e-07!63
|ontology_enrichment_uberon=UBERON:0003914!3.19e-21!117;UBERON:0000490!3.52e-19!148;UBERON:0002100!1.04e-18!199;UBERON:0001637!3.23e-18!42;UBERON:0003509!3.23e-18!42;UBERON:0004572!3.23e-18!42;UBERON:0000475!1.54e-17!264;UBERON:0002049!2.11e-17!78;UBERON:0007798!2.11e-17!78;UBERON:0000486!3.10e-17!83;UBERON:0004872!3.64e-17!83;UBERON:0007500!1.58e-16!59;UBERON:0001981!1.58e-16!59;UBERON:0004537!1.58e-16!59;UBERON:0006965!1.58e-16!59;UBERON:0003104!4.65e-16!160;UBERON:0009142!4.65e-16!160;UBERON:0005256!7.14e-16!122;UBERON:0004573!1.26e-15!33;UBERON:0004571!1.26e-15!33;UBERON:0007503!1.37e-15!78;UBERON:0002329!1.98e-15!71;UBERON:0003059!1.98e-15!71;UBERON:0007282!1.98e-15!71;UBERON:0004290!1.98e-15!71;UBERON:0009618!1.98e-15!71;UBERON:0000055!6.49e-15!68;UBERON:0007524!1.15e-14!73;UBERON:0003077!1.21e-14!72;UBERON:0007285!1.21e-14!72;UBERON:0001134!1.22e-13!62;UBERON:0002036!1.22e-13!62;UBERON:0003082!1.22e-13!62;UBERON:0004535!2.63e-13!109;UBERON:0002385!4.97e-13!64;UBERON:0001015!4.97e-13!64;UBERON:0000383!4.97e-13!64;UBERON:0001009!1.23e-12!112;UBERON:0000467!6.23e-11!624;UBERON:0000480!1.20e-10!625;UBERON:0000468!2.82e-10!656;UBERON:0003102!4.36e-09!99;UBERON:0000947!6.26e-09!21;UBERON:0010191!6.26e-09!21;UBERON:0000926!1.51e-07!315;UBERON:0004120!1.51e-07!315;UBERON:0006603!1.51e-07!315;UBERON:0000119!1.79e-07!309;UBERON:0000483!3.82e-07!306;UBERON:0002199!4.33e-07!46;UBERON:0002416!4.33e-07!46
|tf_chipseq_enrich=CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0486995669157876!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101218306562916!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00389604518055573!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185448717709486!HMGN3#9324;3:6.13391079251294:0.00664069668332472:0.0282849804612459!IRF1#3659;3:5.72787281517293:0.00809711479033333:0.0319814904919303!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00793978626220362!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321084345758641!TAF7#6879;4:11.4330694049239:5.85061525419808e-05:0.000966976430658638!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00345796094192434!ZEB1#6935;3:12.6663240131579:0.00079333607591285:0.00612879846381109
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}}
}}

Revision as of 12:00, 19 October 2012


Full id: C2058_Smooth_basal_mesenchymal_tubular_Renal_lung_Urothelial



Phase1 CAGE Peaks

Hg19::chr10:33246815..33246830,-p4@ITGB1
Hg19::chr10:33246846..33246855,-p11@ITGB1
Hg19::chr10:33246856..33246867,-p8@ITGB1
Hg19::chr10:33246874..33246907,-p2@ITGB1


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
epithelial tube3.19e-21117
unilaminar epithelium3.52e-19148
trunk1.04e-18199
artery3.23e-1842
arterial blood vessel3.23e-1842
arterial system3.23e-1842
organism subdivision1.54e-17264
vasculature2.11e-1778
vascular system2.11e-1778
multilaminar epithelium3.10e-1783
splanchnic layer of lateral plate mesoderm3.64e-1783
epithelial tube open at both ends1.58e-1659
blood vessel1.58e-1659
blood vasculature1.58e-1659
vascular cord1.58e-1659
mesenchyme4.65e-16160
entire embryonic mesenchyme4.65e-16160
trunk mesenchyme7.14e-16122
systemic artery1.26e-1533
systemic arterial system1.26e-1533
epithelial vesicle1.37e-1578
somite1.98e-1571
presomitic mesoderm1.98e-1571
presumptive segmental plate1.98e-1571
dermomyotome1.98e-1571
trunk paraxial mesoderm1.98e-1571
vessel6.49e-1568
dense mesenchyme tissue1.15e-1473
paraxial mesoderm1.21e-1472
presumptive paraxial mesoderm1.21e-1472
skeletal muscle tissue1.22e-1362
striated muscle tissue1.22e-1362
myotome1.22e-1362
cardiovascular system2.63e-13109
muscle tissue4.97e-1364
musculature4.97e-1364
musculature of body4.97e-1364
circulatory system1.23e-12112
anatomical system6.23e-11624
anatomical group1.20e-10625
multi-cellular organism2.82e-10656
surface structure4.36e-0999
aorta6.26e-0921
aortic system6.26e-0921
mesoderm1.51e-07315
mesoderm-derived structure1.51e-07315
presumptive mesoderm1.51e-07315
cell layer1.79e-07309
epithelium3.82e-07306
integument4.33e-0746
integumental system4.33e-0746
Disease
Ontology termp-valuen
ovarian cancer2.97e-0814


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
CCNT2#90534.752151182721970.01386206996689490.0486995669157876
EGR1#195844.988179094810140.001615011500076050.0101218306562916
GABPB1#255347.067683836182170.0004006876864423170.00389604518055573
HEY1#2346244.040111043105710.00375304636917980.0185448717709486
HMGN3#932436.133910792512940.006640696683324720.0282849804612459
IRF1#365935.727872815172930.008097114790333330.0319814904919303
SIN3A#2594245.408884726815140.001168172384885160.00793978626220362
TAF1#687243.343046285745290.008005664898701650.0321084345758641
TAF7#6879411.43306940492395.85061525419808e-050.000966976430658638
ZBTB7A#5134147.35190930787590.000342223540015990.00345796094192434
ZEB1#6935312.66632401315790.000793336075912850.00612879846381109



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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