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Coexpression cluster:C2744: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487372740371161!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00998346455302453!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378767194514211!GATA1#2623;3:10.1702311078503:0.00151515816849827:0.00966715156452998!GATA2#2624;3:9.5586988001655:0.00181815161835744:0.0109048375851164!HMGN3#9324;3:6.13391079251294:0.00664069668332472:0.0283080702412143!NRF1#4899;3:9.15770958578318:0.00206195379173342:0.0119651290173823!TAL1#6886;3:22.4014625080802:0.000146275639593017:0.00188953389282067!TRIM28#10155;3:13.9428937839469:0.000597285818425842:0.0049955901009511
|tf_chipseq_enrich=CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487372740371161!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00998346455302453!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378767194514211!GATA1#2623;3:10.1702311078503:0.00151515816849827:0.00966715156452998!GATA2#2624;3:9.5586988001655:0.00181815161835744:0.0109048375851164!HMGN3#9324;3:6.13391079251294:0.00664069668332472:0.0283080702412143!NRF1#4899;3:9.15770958578318:0.00206195379173342:0.0119651290173823!TAL1#6886;3:22.4014625080802:0.000146275639593017:0.00188953389282067!TRIM28#10155;3:13.9428937839469:0.000597285818425842:0.0049955901009511
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}}
}}

Revision as of 15:41, 26 November 2012


Full id: C2744_breast_Renal_mature_adipose_lung_Endothelial_heart



Phase1 CAGE Peaks

Hg19::chr3:52479112..52479126,-p1@SEMA3G
Hg19::chr7:1094939..1094950,+p4@GPR146
Hg19::chr7:1094970..1094983,+p5@GPR146
Hg19::chr7:1094987..1095014,+p2@GPR146


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
adult organism6.71e-75114
neural tube2.60e-2756
neural rod2.60e-2756
future spinal cord2.60e-2756
neural keel2.60e-2756
regional part of nervous system1.96e-2553
regional part of brain1.96e-2553
regional part of forebrain2.51e-2141
forebrain2.51e-2141
anterior neural tube2.51e-2141
future forebrain2.51e-2141
neural plate6.54e-2182
presumptive neural plate6.54e-2182
neurectoderm9.41e-2186
brain grey matter1.23e-1834
gray matter1.23e-1834
telencephalon1.91e-1834
brain5.56e-1868
future brain5.56e-1868
central nervous system1.21e-1781
regional part of telencephalon4.25e-1732
cerebral hemisphere5.64e-1732
nervous system3.11e-1689
regional part of cerebral cortex4.52e-1522
pre-chordal neural plate7.33e-1561
ecto-epithelium2.76e-14104
neocortex6.75e-1420
anatomical conduit1.09e-13240
tube6.28e-13192
structure with developmental contribution from neural crest2.15e-12132
cerebral cortex2.16e-1225
pallium2.16e-1225
anatomical cluster4.84e-11373
organ system subdivision5.72e-09223
neural nucleus5.54e-089
nucleus of brain5.54e-089
ectoderm-derived structure5.96e-08171
ectoderm5.96e-08171
presumptive ectoderm5.96e-08171
basal ganglion1.04e-079
nuclear complex of neuraxis1.04e-079
aggregate regional part of brain1.04e-079
collection of basal ganglia1.04e-079
cerebral subcortex1.04e-079
blood vessel endothelium1.91e-0718
endothelium1.91e-0718
cardiovascular system endothelium1.91e-0718
posterior neural tube3.36e-0715
chordal neural plate3.36e-0715


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#90534.752151182721970.01386206996689490.0487372740371161
E2F6#187645.017155731697390.00157802193473060.00998346455302453
GABPB1#255335.300762877136630.01012678824234270.0378767194514211
GATA1#2623310.17023110785030.001515158168498270.00966715156452998
GATA2#262439.55869880016550.001818151618357440.0109048375851164
HMGN3#932436.133910792512940.006640696683324720.0283080702412143
NRF1#489939.157709585783180.002061953791733420.0119651290173823
TAL1#6886322.40146250808020.0001462756395930170.00188953389282067
TRIM28#10155313.94289378394690.0005972858184258420.0049955901009511



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.