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Coexpression cluster:C1584: Difference between revisions

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|tf_chipseq_enrich=EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110643077276695!FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000388397630134327!FOSL2#2355;5:16.9302006045617:7.18315284751475e-07:3.20461896728575e-05!FOXA1#3169;5:11.0814197493855:5.98116883436141e-06:0.000178680575483945!GATA2#2624;5:12.744931733554:2.9719152914525e-06:0.000100970677008461!GATA3#2625;3:16.3419098143236:0.000467886519508923:0.00430117069016745!JUN#3725;5:12.5128291923363:3.25800591331781e-06:0.00010898875066656!JUND#3727;5:6.99466394187103:5.97069468343598e-05:0.000982934082666094!MAFF#23764;5:56.3153564899452:1.76021388477016e-09:1.53965643141968e-07!MAFK#7975;5:27.1007331378299:6.83095404221442e-08:4.14777912334205e-06!NR3C1#2908;5:14.973023331173:1.32777388277837e-06:5.23485755166062e-05!STAT3#6774;5:10.5194649971542:7.759040745861e-06:0.000220083230976908!TCF7L2#6934;5:10.7701765631373:6.89693748574565e-06:0.00019936597123548
|tf_chipseq_enrich=EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110643077276695!FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000388397630134327!FOSL2#2355;5:16.9302006045617:7.18315284751475e-07:3.20461896728575e-05!FOXA1#3169;5:11.0814197493855:5.98116883436141e-06:0.000178680575483945!GATA2#2624;5:12.744931733554:2.9719152914525e-06:0.000100970677008461!GATA3#2625;3:16.3419098143236:0.000467886519508923:0.00430117069016745!JUN#3725;5:12.5128291923363:3.25800591331781e-06:0.00010898875066656!JUND#3727;5:6.99466394187103:5.97069468343598e-05:0.000982934082666094!MAFF#23764;5:56.3153564899452:1.76021388477016e-09:1.53965643141968e-07!MAFK#7975;5:27.1007331378299:6.83095404221442e-08:4.14777912334205e-06!NR3C1#2908;5:14.973023331173:1.32777388277837e-06:5.23485755166062e-05!STAT3#6774;5:10.5194649971542:7.759040745861e-06:0.000220083230976908!TCF7L2#6934;5:10.7701765631373:6.89693748574565e-06:0.00019936597123548
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}}
}}

Revision as of 14:59, 26 November 2012


Full id: C1584_Endothelial_prostate_Gingival_Prostate_lens_Urothelial_Mallassezderived



Phase1 CAGE Peaks

Hg19::chr10:4720273..4720297,-p1@LOC100216001
Hg19::chr10:4720301..4720325,-p1@ENST00000449712
Hg19::chr10:4720333..4720350,-p3@ENST00000430998
Hg19::chr10:4720356..4720386,-p2@ENST00000430998
Hg19::chr10:4720389..4720416,-p1@ENST00000430998


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
blood vessel endothelium7.44e-2318
endothelium7.44e-2318
cardiovascular system endothelium7.44e-2318
simple squamous epithelium5.98e-2222
squamous epithelium2.30e-1825
vessel6.33e-1668
epithelial tube open at both ends1.22e-1259
blood vessel1.22e-1259
blood vasculature1.22e-1259
vascular cord1.22e-1259
endothelial tube2.22e-129
arterial system endothelium2.22e-129
endothelium of artery2.22e-129
vasculature2.75e-1278
vascular system2.75e-1278
splanchnic layer of lateral plate mesoderm1.44e-1183
epithelial tube5.04e-11117
unilaminar epithelium5.78e-10148
cardiovascular system6.70e-09109
circulatory system2.43e-08112
artery6.87e-0842
arterial blood vessel6.87e-0842
arterial system6.87e-0842
multi-cellular organism1.71e-07656
anatomical system2.65e-07624
aorta2.71e-0721
aortic system2.71e-0721
anatomical group3.14e-07625
surface structure3.49e-0799
anatomical conduit4.81e-07240
systemic artery7.16e-0733
systemic arterial system7.16e-0733


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
EP300#203356.77394172622327.00901578206049e-050.00110643077276695
FOS#235358.99795530889441.69470025615156e-050.000388397630134327
FOSL2#2355516.93020060456177.18315284751475e-073.20461896728575e-05
FOXA1#3169511.08141974938555.98116883436141e-060.000178680575483945
GATA2#2624512.7449317335542.9719152914525e-060.000100970677008461
GATA3#2625316.34190981432360.0004678865195089230.00430117069016745
JUN#3725512.51282919233633.25800591331781e-060.00010898875066656
JUND#372756.994663941871035.97069468343598e-050.000982934082666094
MAFF#23764556.31535648994521.76021388477016e-091.53965643141968e-07
MAFK#7975527.10073313782996.83095404221442e-084.14777912334205e-06
NR3C1#2908514.9730233311731.32777388277837e-065.23485755166062e-05
STAT3#6774510.51946499715427.759040745861e-060.000220083230976908
TCF7L2#6934510.77017656313736.89693748574565e-060.00019936597123548



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.