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Coexpression cluster:C2486: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2486_optic_Adipocyte_aorta_embryonic_diencephalon_basal_corpus
|full_id=C2486_optic_Adipocyte_aorta_embryonic_diencephalon_basal_corpus
|id=C2486
|id=C2486

Revision as of 15:13, 12 September 2012


Full id: C2486_optic_Adipocyte_aorta_embryonic_diencephalon_basal_corpus



Phase1 CAGE Peaks

Hg19::chr19:38743538..38743565,+p@chr19:38743538..38743565
+
Hg19::chr19:38746979..38747050,-p1@PPP1R14A
Hg19::chr19:38747153..38747169,-p3@PPP1R14A
Hg19::chr19:38747174..38747218,-p2@PPP1R14A


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism9.45e-40115
neural tube5.47e-2257
neural rod5.47e-2257
future spinal cord5.47e-2257
neural keel5.47e-2257
regional part of brain1.22e-2059
neural plate1.07e-1986
presumptive neural plate1.07e-1986
central nervous system1.17e-1782
neurectoderm1.38e-1790
regional part of nervous system2.77e-1794
nervous system2.77e-1794
organism subdivision6.64e-17365
anterior neural tube6.17e-1642
brain1.20e-1569
future brain1.20e-1569
regional part of forebrain1.55e-1541
forebrain1.55e-1541
future forebrain1.55e-1541
gray matter7.84e-1534
brain grey matter7.84e-1534
telencephalon8.49e-1534
pre-chordal neural plate1.15e-1461
ectoderm-derived structure1.15e-14169
regional part of telencephalon3.08e-1433
head5.46e-14123
cell layer7.09e-14312
tube1.02e-13194
ectoderm1.63e-13173
presumptive ectoderm1.63e-13173
cerebral hemisphere1.67e-1332
anatomical conduit2.25e-13241
epithelium2.25e-13309
anterior region of body4.70e-13129
craniocervical region4.70e-13129
multi-tissue structure2.98e-12347
organ part1.15e-11219
anatomical cluster1.55e-11286
cerebral cortex6.55e-1025
pallium6.55e-1025
regional part of cerebral cortex7.01e-1022
neocortex5.73e-0920
anatomical space1.41e-08104
multi-cellular organism3.09e-08659
anatomical cavity6.06e-0870
body cavity precursor1.04e-0763
compound organ1.53e-0769
posterior neural tube2.63e-0715
chordal neural plate2.63e-0715
immaterial anatomical entity4.65e-07126


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
CTCFL#140690314.80985576923080.0004996291767563340.00440902168071438
HMGN3#932436.133910792512940.006640696683324720.0282953661992473
NR3C1#2908311.22976749837980.001131672068063850.00775478637336926
NRF1#489939.157709585783180.002061953791733420.0119624703952254
RAD21#588537.766275421592250.0033411193858720.0172675755909089
SMC3#9126311.28369963369960.001115802366868050.00765658892203238
ZBTB7A#5134135.513931980906920.009038352821081090.0342459922464406



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.