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Coexpression cluster:C2156: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2156_Mesenchymal_Smooth_leiomyoma_Fibroblast_Myoblast_Preadipocyte_Hair
|full_id=C2156_Mesenchymal_Smooth_leiomyoma_Fibroblast_Myoblast_Preadipocyte_Hair
|id=C2156
|id=C2156

Revision as of 14:50, 12 September 2012


Full id: C2156_Mesenchymal_Smooth_leiomyoma_Fibroblast_Myoblast_Preadipocyte_Hair



Phase1 CAGE Peaks

Hg19::chr11:65687158..65687216,+p4@DRAP1
Hg19::chr11:65687222..65687240,+p7@DRAP1
Hg19::chr11:65687243..65687276,+p8@DRAP1
Hg19::chr11:65687362..65687436,+p3@DRAP1


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><br>


Uber Anatomy
Ontology termp-valuen
somite2.01e-2383
paraxial mesoderm2.01e-2383
presomitic mesoderm2.01e-2383
presumptive segmental plate2.01e-2383
trunk paraxial mesoderm2.01e-2383
presumptive paraxial mesoderm2.01e-2383
multilaminar epithelium6.65e-2082
dermomyotome9.87e-2070
artery1.01e-1742
arterial blood vessel1.01e-1742
arterial system1.01e-1742
skeletal muscle tissue5.51e-1661
striated muscle tissue5.51e-1661
myotome5.51e-1661
systemic artery5.62e-1533
systemic arterial system5.62e-1533
muscle tissue1.55e-1463
musculature1.55e-1463
musculature of body1.55e-1463
vessel3.31e-1469
blood vessel7.41e-1460
epithelial tube open at both ends7.41e-1460
blood vasculature7.41e-1460
vascular cord7.41e-1460
trunk mesenchyme8.32e-14143
vasculature9.93e-1479
vascular system9.93e-1479
surface structure4.76e-1395
splanchnic layer of lateral plate mesoderm1.86e-1184
cardiovascular system7.02e-11110
integument1.19e-0945
integumental system1.19e-0945
circulatory system1.94e-09113
unilaminar epithelium2.25e-09138
trunk7.92e-09216
skin of body2.09e-0840
aorta5.07e-0821
aortic system5.07e-0821
epithelial tube9.95e-08118
organism subdivision9.14e-07365


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
BCL11A#53335214.18472755180350.007108328585298740.0296149165916713
BCL3#602217.27355140186920.004834494208076070.0226711750975375
BCLAF1#9774316.23948570759140.000380256706766480.00376539586593196
CCNT2#90534.752151182721970.01386206996689490.0487028434795308
E2F6#187645.017155731697390.00157802193473060.00995151457287175
EBF1#187936.679850134926750.005184294118278910.0240352684964235
EGR1#195844.988179094810140.001615011500076050.0101285165469551
EP300#203335.08045629466740.01144298405398240.0418714109597739
ETS1#211337.296570691651750.00400857377511390.0191980298298308
FOSL1#8061329.78518478727986.26173959487248e-050.00102487043025997
GABPB1#255335.300762877136630.01012678824234270.0378401301338831
GATA3#2625213.6182581786030.00769665208093340.03168804536132
HDAC2#3066310.06171517746970.00156372754474740.00992127702119396
HNF4A#3172211.56614518147680.01057585681762490.0390597605974938
HNF4G#3174321.56506689483510.0001638032421292610.00203538926885638
JUND#372735.245997956403270.01043432751748420.0386696970156678
MAX#414946.452555509007120.0005767613195645490.00484526829584958
MEF2C#4208220.6556772463120.003402570579445040.0173550043341796
MXI1#460137.471178721569470.003741314738550960.0186234769543646
MYC#460945.22228187160940.001344309395272740.00885793873393624
NR2C2#7182324.46095817893070.0001125906063438030.00155499211001593
PAX5#507946.669565531177830.0005052774169483260.0044322751678705
PBX3#5090210.95725634337210.01174530180688030.0428216007613201
SMC3#9126311.28369963369960.001115802366868050.00765457720660357
SP2#6668213.07676524692230.008330036536614940.0328022278051251
STAT1#6772315.52994062289940.000434088655175550.00404819939797118
STAT2#6773232.63188559322030.001379588775125520.0089810429523988
TCF7L2#693438.077632422353010.002978381685834620.0158574227613622



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.