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Coexpression cluster:C4619: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4619_smooth_bladder_left_Synoviocyte_Fibroblast_Hep2_heart
|full_id=C4619_smooth_bladder_left_Synoviocyte_Fibroblast_Hep2_heart
|id=C4619
|id=C4619

Revision as of 17:43, 12 September 2012


Full id: C4619_smooth_bladder_left_Synoviocyte_Fibroblast_Hep2_heart



Phase1 CAGE Peaks

Hg19::chr6:57037421..57037481,+p2@BAG2
Hg19::chr6:57037487..57037509,+p3@BAG2
Hg19::chr6:57037538..57037554,+p4@BAG2


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
fibroblast2.33e-1375
non-terminally differentiated cell6.95e-13180
skin fibroblast2.96e-1023
Uber Anatomy
Ontology termp-valuen
somite2.44e-0883
paraxial mesoderm2.44e-0883
presomitic mesoderm2.44e-0883
presumptive segmental plate2.44e-0883
trunk paraxial mesoderm2.44e-0883
presumptive paraxial mesoderm2.44e-0883
mesenchyme1.27e-07238
entire embryonic mesenchyme1.27e-07238
trunk mesenchyme1.58e-07143
dermomyotome8.61e-0770
larynx9.17e-079
Disease
Ontology termp-valuen
disease of cellular proliferation5.10e-07239


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#90536.336201576962630.003930750035764890.0191056733366803
CTCF#1066435.360256373075030.0064925092527670.0281159005618333
CTCFL#140690319.74647435897440.0001298372005551160.0017230072920935
E2F1#186934.907389214879320.008460985347239390.0327498646757221
E2F6#187635.017155731697390.00791769806886330.0324141142493048
EGR1#195834.988179094810140.008056488137383440.0322330510488886
EP300#203336.77394172622320.003216880500103790.0168328965654762
FOSL2#2355316.93020060456170.0002060162053171620.00243974673626478
FOXA1#3169311.08141974938550.000734755275698670.0058395180152723
GTF2B#2959331.94382993432423.06634405746243e-050.000629537855351522
HMGN3#932438.178547723350590.001827766942164210.0109142453786557
JUND#372736.994663941871030.002921845042734990.0157613023303651
MYC#460935.22228187160940.007020843755740150.0295903914853005
NFKB1#479035.488063424193840.006049381815655430.0270783210802862
PAX5#507936.669565531177830.003370290999677260.0173624930555563
POU2F2#545239.106124057742520.001324165192682130.00885481422451844
RAD21#5885310.35503389545630.0009004912073565420.00668180470373782
RFX5#5993312.04791082719510.0005717246050312580.00486676550858746
SIN3A#2594235.408884726815140.006318961977991520.0278153110519875
SIX5#147912317.0867153554590.0002004060546325010.00240300894830813
SP1#666735.69838137814090.005403962701712170.0247787004699529
SRF#6722313.79717826216780.0003806615025800190.00376298217396636
TAF7#6879311.43306940492390.0006690181981945830.00545488262949833
TCF12#6938310.63446490218640.0008313523990202070.00631872594434694
TCF7L2#6934310.77017656313730.0008003181298398380.00617086933645942
TFAP2A#7020316.5186343730450.0002218033880766340.00249353326666691
TFAP2C#7022310.80922860986020.0007916746575753130.00618689835098085
YY1#752834.911170749853860.008441455341808260.0331074075047171
ZBTB7A#5134137.35190930787590.002516255860282270.0140863660909101
ZEB1#6935316.88843201754390.0002075486917327580.00243716863232263
ZNF263#1012738.221841637010680.001799043925565870.0110070502953822



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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