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Coexpression cluster:C490: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C490_Hair_Fibroblast_Synoviocyte_Olfactory_Preadipocyte_Endothelial_Osteoblast
|full_id=C490_Hair_Fibroblast_Synoviocyte_Olfactory_Preadipocyte_Endothelial_Osteoblast
|id=C490
|id=C490

Revision as of 18:02, 12 September 2012


Full id: C490_Hair_Fibroblast_Synoviocyte_Olfactory_Preadipocyte_Endothelial_Osteoblast



Phase1 CAGE Peaks

Hg19::chr10:17271510..17271558,-p2@uc001iot.1
Hg19::chr10:17271561..17271615,-p4@uc001iot.1
Hg19::chr10:17271691..17271750,-p3@uc001iot.1
Hg19::chr10:17271757..17271791,-p6@uc001iot.1
Hg19::chr10:17271821..17271858,-p7@uc001iot.1
Hg19::chr10:17271866..17271897,-p5@uc001iot.1
Hg19::chr10:17272666..17272724,-p@chr10:17272666..17272724
-
Hg19::chr10:17275793..17275820,-p@chr10:17275793..17275820
-
Hg19::chr10:17275853..17275926,-p@chr10:17275853..17275926
-
Hg19::chr10:17276719..17276781,-p1@ENST00000456355
Hg19::chr10:17276801..17276827,-p5@ENST00000456355
Hg19::chr10:17277201..17277219,-p4@ENST00000456355
Hg19::chr10:17277221..17277254,-p3@ENST00000456355
Hg19::chr10:17277255..17277323,-p2@ENST00000456355
Hg19::chr10:17277365..17277388,-p@chr10:17277365..17277388
-
Hg19::chr10:17278325..17278353,-p@chr10:17278325..17278353
-
Hg19::chr10:17278354..17278389,-p@chr10:17278354..17278389
-
Hg19::chr10:17279298..17279334,-p1@CU674071
Hg19::chr10:17279393..17279433,-p2@CU674071


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
lateral plate mesoderm4.31e-20216
musculoskeletal system5.87e-20167
somite7.51e-1883
paraxial mesoderm7.51e-1883
presomitic mesoderm7.51e-1883
presumptive segmental plate7.51e-1883
trunk paraxial mesoderm7.51e-1883
presumptive paraxial mesoderm7.51e-1883
vasculature1.13e-1779
vascular system1.13e-1779
cardiovascular system1.15e-17110
circulatory system1.66e-16113
dermomyotome2.44e-1670
splanchnic layer of lateral plate mesoderm2.07e-1584
vessel3.22e-1569
blood vessel2.56e-1460
epithelial tube open at both ends2.56e-1460
blood vasculature2.56e-1460
vascular cord2.56e-1460
multilaminar epithelium6.12e-1482
artery1.65e-1342
arterial blood vessel1.65e-1342
arterial system1.65e-1342
mesoderm3.66e-13448
mesoderm-derived structure3.66e-13448
presumptive mesoderm3.66e-13448
skeletal muscle tissue1.58e-1261
striated muscle tissue1.58e-1261
myotome1.58e-1261
muscle tissue7.77e-1263
musculature7.77e-1263
musculature of body7.77e-1263
connective tissue8.06e-11375
systemic artery1.65e-1033
systemic arterial system1.65e-1033
epithelial tube2.87e-08118
trunk mesenchyme9.33e-08143
skeletal element9.54e-08101
skeletal system9.54e-08101
integument1.60e-0745
integumental system1.60e-0745
multi-cellular organism1.99e-07659
aorta3.52e-0721
aortic system3.52e-0721
adipose tissue4.48e-0714


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
CTCF#10664154.23178134716452.07084251553897e-081.47427894669649e-06
POLR2A#5430171.921405473762480.0001223247950698280.00164866166889893
SETDB1#986948.488426563791680.001086656417664370.0075983737014227
SP1#666792.699233284382530.002657474221002050.0146662412897502
ZBTB33#1000958.332822376310830.0002516066894176260.00271014346494301



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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