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Coexpression cluster:C4202: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00129802898279646!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326289361450533!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323140472299341!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186998104073149!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000739095875017222!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246325937737816!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190775202649526!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00422330360892503
|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00129802898279646!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326289361450533!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323140472299341!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186998104073149!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000739095875017222!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246325937737816!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190775202649526!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00422330360892503
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}}
}}

Revision as of 16:36, 26 November 2012


Full id: C4202_Hepatic_Astrocyte_testicular_teratocarcinoma_synovial_basal_prostate



Phase1 CAGE Peaks

Hg19::chr2:237076971..237076978,-p3@GBX2
Hg19::chr2:237076992..237077008,-p2@GBX2
Hg19::chr2:237077022..237077038,-p1@GBX2


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>

Uber Anatomy
Ontology termp-valuen
posterior neural tube1.64e-1515
chordal neural plate1.64e-1515
segmental subdivision of hindbrain3.29e-1412
hindbrain3.29e-1412
presumptive hindbrain3.29e-1412
segmental subdivision of nervous system6.94e-1313
endothelial tube1.09e-119
arterial system endothelium1.09e-119
endothelium of artery1.09e-119
blood vessel endothelium5.24e-1118
endothelium5.24e-1118
cardiovascular system endothelium5.24e-1118
regional part of metencephalon1.80e-109
metencephalon1.80e-109
future metencephalon1.80e-109
brainstem1.53e-086
squamous epithelium1.68e-0825
central nervous system1.70e-0881
simple squamous epithelium2.08e-0822
nervous system4.07e-0889
neural tube6.95e-0856
neural rod6.95e-0856
future spinal cord6.95e-0856
neural keel6.95e-0856
tube1.86e-07192
cerebellum2.52e-076
rhombic lip2.52e-076
brain3.17e-0768
future brain3.17e-0768
regional part of nervous system9.04e-0753
regional part of brain9.04e-0753
Disease
Ontology termp-valuen
cell type cancer9.08e-11143
carcinoma5.85e-10106
cancer1.58e-08235
disease of cellular proliferation4.85e-08239


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
ATF3#467322.46317452600878.81932387510763e-050.00129802898279646
E2F1#186934.907389214879320.008460985347239390.0326289361450533
E2F6#187635.017155731697390.00791769806886330.0323140472299341
MAX#414936.452555509007120.003721913834265510.0186998104073149
NANOG#79923329.24477848101273.99627955670032e-050.000739095875017222
NFYB#4801316.75979325353650.0002123649923296180.00246325937737816
USF1#739136.361499277207960.00388404057290560.0190775202649526
USF2#7392312.99219738506960.0004558979393427810.00422330360892503



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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