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Coexpression cluster:C1941: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;4:6.37691810065985:0.00111394417667732:0.00765792626829925!EP300#2033;4:5.41915338097856:0.0020938692794389:0.0121254013681907!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.0038689616474957!YY1#7528;4:3.92893659988308:0.00719386626991762:0.0298545736058144
|tf_chipseq_enrich=CEBPB#1051;4:6.37691810065985:0.00111394417667732:0.00765792626829925!EP300#2033;4:5.41915338097856:0.0020938692794389:0.0121254013681907!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.0038689616474957!YY1#7528;4:3.92893659988308:0.00719386626991762:0.0298545736058144
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}}
}}

Revision as of 15:12, 26 November 2012


Full id: C1941_Fibroblast_Nucleus_Mesenchymal_tenocyte_Anulus_Smooth_acute



Phase1 CAGE Peaks

Hg19::chr4:55095379..55095390,+p6@PDGFRA
Hg19::chr4:55095396..55095422,+p3@PDGFRA
Hg19::chr4:55095428..55095475,+p2@PDGFRA
Hg19::chr4:55095476..55095494,+p4@PDGFRA
Hg19::chr4:55162545..55162559,+p@chr4:55162545..55162559
+


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 tissue3.81e-1873
somite1.23e-1771
presomitic mesoderm1.23e-1771
presumptive segmental plate1.23e-1771
dermomyotome1.23e-1771
trunk paraxial mesoderm1.23e-1771
paraxial mesoderm1.29e-1772
presumptive paraxial mesoderm1.29e-1772
multi-tissue structure2.97e-16342
muscle tissue1.92e-1564
musculature1.92e-1564
musculature of body1.92e-1564
skeletal muscle tissue4.58e-1562
striated muscle tissue4.58e-1562
myotome4.58e-1562
epithelial vesicle3.45e-1478
multilaminar epithelium5.74e-1483
structure with developmental contribution from neural crest1.85e-13132
mesenchyme7.39e-12160
entire embryonic mesenchyme7.39e-12160
multi-cellular organism6.97e-11656
trunk mesenchyme1.17e-10122
adult organism1.25e-10114
anatomical cluster2.87e-10373
primary circulatory organ7.47e-1027
heart1.54e-0924
primitive heart tube1.54e-0924
primary heart field1.54e-0924
anterior lateral plate mesoderm1.54e-0924
heart tube1.54e-0924
heart primordium1.54e-0924
cardiac mesoderm1.54e-0924
cardiogenic plate1.54e-0924
heart rudiment1.54e-0924
tissue6.37e-09773
surface structure6.79e-0999
cell layer2.01e-08309
splanchnic layer of lateral plate mesoderm2.42e-0883
epithelium2.53e-08306
anatomical group5.14e-08625
anatomical system6.18e-08624
integument1.00e-0746
integumental system1.00e-0746
systemic artery2.40e-0733
systemic arterial system2.40e-0733
organism subdivision3.58e-07264
skin of body9.75e-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
CEBPB#105146.376918100659850.001113944176677320.00765792626829925
EP300#203345.419153380978560.00209386927943890.0121254013681907
RAD21#588548.284027116365060.0004011622639122450.0038689616474957
YY1#752843.928936599883080.007193866269917620.0298545736058144



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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