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Coexpression cluster:C856: Difference between revisions

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|tf_chipseq_enrich=GATA2#2624;5:6.372465866777:0.000534886507521368:0.00462289076125655!TRIM28#10155;3:5.57715751357876:0.0140319780523358:0.04925009261352
|tf_chipseq_enrich=GATA2#2624;5:6.372465866777:0.000534886507521368:0.00462289076125655!TRIM28#10155;3:5.57715751357876:0.0140319780523358:0.04925009261352
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}}
}}

Revision as of 14:31, 26 November 2012


Full id: C856_Endothelial_lung_diaphragm_left_kidney_heart_Hepatic



Phase1 CAGE Peaks

Hg19::chr2:197226875..197226907,-p3@HECW2
Hg19::chr4:101439078..101439098,-p3@EMCN
Hg19::chr4:101439101..101439106,-p7@EMCN
Hg19::chr4:101439116..101439130,-p2@EMCN
Hg19::chr4:101439148..101439199,-p1@EMCN
Hg19::chr6:46922659..46922725,-p1@GPR116
Hg19::chr6:76203560..76203582,-p4@FILIP1
Hg19::chr6:76203624..76203635,-p7@FILIP1
Hg19::chr8:68864263..68864328,+p2@PREX2
Hg19::chrX:71299835..71299852,+p@chrX:71299835..71299852
+


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 organism1.51e-68114
anatomical conduit2.27e-29240
neural tube7.54e-2656
neural rod7.54e-2656
future spinal cord7.54e-2656
neural keel7.54e-2656
tube1.24e-25192
anatomical cluster2.94e-25373
regional part of nervous system1.76e-2353
regional part of brain1.76e-2353
regional part of forebrain5.30e-2141
forebrain5.30e-2141
anterior neural tube5.30e-2141
future forebrain5.30e-2141
blood vessel endothelium1.58e-1918
endothelium1.58e-1918
cardiovascular system endothelium1.58e-1918
neural plate9.46e-1982
presumptive neural plate9.46e-1982
neurectoderm3.43e-1786
central nervous system4.01e-1781
structure with developmental contribution from neural crest6.39e-17132
telencephalon3.13e-1634
brain grey matter3.30e-1634
gray matter3.30e-1634
brain3.65e-1668
future brain3.65e-1668
regional part of telencephalon4.75e-1532
cerebral hemisphere5.16e-1532
simple squamous epithelium7.74e-1522
nervous system8.74e-1589
regional part of cerebral cortex2.64e-1422
cell layer2.36e-13309
epithelium2.55e-13306
neocortex5.49e-1320
ecto-epithelium1.05e-12104
vessel1.47e-1268
organ system subdivision1.72e-12223
squamous epithelium2.45e-1225
cerebral cortex5.87e-1225
pallium5.87e-1225
pre-chordal neural plate7.11e-1261
multi-cellular organism8.72e-12656
splanchnic layer of lateral plate mesoderm1.57e-1083
anatomical system3.35e-10624
anatomical group4.07e-10625
multi-tissue structure5.98e-10342
endothelial tube7.84e-109
arterial system endothelium7.84e-109
endothelium of artery7.84e-109
vasculature1.34e-0978
vascular system1.34e-0978
circulatory system2.84e-09112
epithelial tube open at both ends3.32e-0959
blood vessel3.32e-0959
blood vasculature3.32e-0959
vascular cord3.32e-0959
compound organ1.74e-0868
embryonic structure3.91e-08564
embryo4.50e-08592
germ layer5.43e-08560
germ layer / neural crest5.43e-08560
embryonic tissue5.43e-08560
presumptive structure5.43e-08560
germ layer / neural crest derived structure5.43e-08560
epiblast (generic)5.43e-08560
cardiovascular system6.69e-08109
epithelial tube8.96e-08117
lymphoid system9.88e-0810
developing anatomical structure1.12e-07581
organ part1.85e-07218
ectoderm-derived structure3.98e-07171
ectoderm3.98e-07171
presumptive ectoderm3.98e-07171


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
GATA2#262456.3724658667770.0005348865075213680.00462289076125655
TRIM28#1015535.577157513578760.01403197805233580.04925009261352



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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