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Coexpression cluster:C1617: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;5:7.97114762582482:3.10621793420244e-05:0.000628215133288475!EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110676534512037!FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000388568166964243!GATA2#2624;5:12.744931733554:2.9719152914525e-06:0.000101003534371626!NR3C1#2908;5:14.973023331173:1.32777388277837e-06:5.23683446161216e-05!STAT3#6774;5:10.5194649971542:7.759040745861e-06:0.000220143019955712!TCF7L2#6934;5:10.7701765631373:6.89693748574565e-06:0.00019947639270944
|tf_chipseq_enrich=CEBPB#1051;5:7.97114762582482:3.10621793420244e-05:0.000628215133288475!EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110676534512037!FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000388568166964243!GATA2#2624;5:12.744931733554:2.9719152914525e-06:0.000101003534371626!NR3C1#2908;5:14.973023331173:1.32777388277837e-06:5.23683446161216e-05!STAT3#6774;5:10.5194649971542:7.759040745861e-06:0.000220143019955712!TCF7L2#6934;5:10.7701765631373:6.89693748574565e-06:0.00019947639270944
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}}
}}

Revision as of 15:00, 26 November 2012


Full id: C1617_Fibroblast_meningioma_giant_Smooth_mesenchymal_hepatic_Olfactory



Phase1 CAGE Peaks

Hg19::chr11:122051194..122051210,-p5@ENST00000533109
Hg19::chr11:122051212..122051237,-p4@ENST00000533109
Hg19::chr11:122051243..122051257,-p3@ENST00000533109
Hg19::chr11:122051315..122051326,-p6@ENST00000533109
Hg19::chr11:122051327..122051348,-p2@ENST00000533109


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
multilaminar epithelium2.98e-2183
somite5.16e-2171
presomitic mesoderm5.16e-2171
presumptive segmental plate5.16e-2171
dermomyotome5.16e-2171
trunk paraxial mesoderm5.16e-2171
dense mesenchyme tissue2.09e-2073
paraxial mesoderm2.40e-2072
presumptive paraxial mesoderm2.40e-2072
epithelial vesicle3.81e-1878
skeletal muscle tissue1.60e-1762
striated muscle tissue1.60e-1762
myotome1.60e-1762
muscle tissue2.86e-1664
musculature2.86e-1664
musculature of body2.86e-1664
unilaminar epithelium1.48e-15148
surface structure1.79e-1499
vasculature1.25e-1278
vascular system1.25e-1278
organism subdivision2.13e-12264
cell layer3.45e-12309
artery8.29e-1242
arterial blood vessel8.29e-1242
arterial system8.29e-1242
epithelium1.97e-11306
trunk mesenchyme3.87e-11122
skin of body8.48e-1141
systemic artery5.40e-1033
systemic arterial system5.40e-1033
cardiovascular system5.94e-10109
integument6.34e-1046
integumental system6.34e-1046
splanchnic layer of lateral plate mesoderm7.56e-1083
mesenchyme1.06e-09160
entire embryonic mesenchyme1.06e-09160
circulatory system4.39e-09112
epithelial tube open at both ends6.24e-0959
blood vessel6.24e-0959
blood vasculature6.24e-0959
vascular cord6.24e-0959
vessel1.05e-0868
trunk6.71e-08199
subdivision of skeletal system1.60e-0716
head3.46e-0756
multi-tissue structure5.23e-07342
subdivision of head6.14e-0749
aorta8.80e-0721
aortic system8.80e-0721


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
CEBPB#105157.971147625824823.10621793420244e-050.000628215133288475
EP300#203356.77394172622327.00901578206049e-050.00110676534512037
FOS#235358.99795530889441.69470025615156e-050.000388568166964243
GATA2#2624512.7449317335542.9719152914525e-060.000101003534371626
NR3C1#2908514.9730233311731.32777388277837e-065.23683446161216e-05
STAT3#6774510.51946499715427.759040745861e-060.000220143019955712
TCF7L2#6934510.77017656313736.89693748574565e-060.00019947639270944



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.