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Coexpression cluster:C2133: Difference between revisions

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|tf_chipseq_enrich=HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185536499929362!IRF1#3659;3:5.72787281517293:0.00809711479033333:0.0319827000335699!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391022965442405!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188049261612439!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00794237065978913!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00119871843200568
|tf_chipseq_enrich=HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185536499929362!IRF1#3659;3:5.72787281517293:0.00809711479033333:0.0319827000335699!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391022965442405!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188049261612439!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00794237065978913!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00119871843200568
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}}
}}

Revision as of 15:18, 26 November 2012


Full id: C2133_Mesenchymal_Fibroblast_Smooth_osteoclastoma_Osteoblast_Prostate_leiomyoma



Phase1 CAGE Peaks

Hg19::chr11:46299186..46299195,+p3@CREB3L1
Hg19::chr11:46299199..46299233,+p1@CREB3L1
Hg19::chr11:46299443..46299459,+p4@CREB3L1
Hg19::chr11:46299539..46299620,+p2@CREB3L1


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
dense mesenchyme tissue1.66e-2573
somite3.49e-2571
presomitic mesoderm3.49e-2571
presumptive segmental plate3.49e-2571
dermomyotome3.49e-2571
trunk paraxial mesoderm3.49e-2571
paraxial mesoderm7.42e-2572
presumptive paraxial mesoderm7.42e-2572
epithelial vesicle7.85e-2478
skeletal muscle tissue8.90e-2362
striated muscle tissue8.90e-2362
myotome8.90e-2362
muscle tissue1.05e-2264
musculature1.05e-2264
musculature of body1.05e-2264
multilaminar epithelium1.28e-2083
mesenchyme1.98e-20160
entire embryonic mesenchyme1.98e-20160
trunk mesenchyme4.91e-20122
unilaminar epithelium3.98e-14148
splanchnic layer of lateral plate mesoderm7.39e-1383
multi-tissue structure1.07e-12342
organism subdivision1.16e-12264
artery7.50e-1242
arterial blood vessel7.50e-1242
arterial system7.50e-1242
trunk1.53e-10199
systemic artery1.94e-1033
systemic arterial system1.94e-1033
vasculature2.95e-1078
vascular system2.95e-1078
surface structure1.83e-0999
epithelial tube open at both ends8.50e-0959
blood vessel8.50e-0959
blood vasculature8.50e-0959
vascular cord8.50e-0959
multi-cellular organism9.33e-09656
cell layer9.42e-09309
epithelium2.04e-08306
epithelial tube5.83e-08117
integument6.54e-0846
integumental system6.54e-0846
vessel1.70e-0768
smooth muscle tissue3.61e-0715
cardiovascular system5.18e-07109
circulatory system5.59e-07112
skin of body7.28e-0741


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
HEY1#2346244.040111043105710.00375304636917980.0185536499929362
IRF1#365935.727872815172930.008097114790333330.0319827000335699
JUND#372746.994663941871030.000417684217818580.00391022965442405
POU2F2#545249.106124057742520.000145395665174930.00188049261612439
SIN3A#2594245.408884726815140.001168172384885160.00794237065978913
TCF12#6938410.63446490218647.8163066689251e-050.00119871843200568



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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