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Coexpression cluster:C4454

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Full id: C4454_Preadipocyte_Chondrocyte_Adipocyte_tenocyte_Ewing_Fibroblast_Smooth



Phase1 CAGE Peaks

Hg19::chr5:122372354..122372440,-p1@PPIC
Hg19::chr7:32996997..32997094,+p1@FKBP9
Hg19::chr7:32997098..32997114,+p2@FKBP9


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


GO IDGO nameFDR corrected p-value
GO:0003755peptidyl-prolyl cis-trans isomerase activity0.000114914022548021
GO:0016859cis-trans isomerase activity0.000114914022548021
GO:0016853isomerase activity0.000796984349929822
GO:0006457protein folding0.000796984349929822
GO:0016018cyclosporin A binding0.002189877685791
GO:0008144drug binding0.00608174002924203
GO:0051082unfolded protein binding0.0473062726156019
GO:0042277peptide binding0.0473062726156019



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
organism subdivision4.42e-17365
trunk1.24e-16216
multi-cellular organism1.66e-15659
trunk mesenchyme2.64e-14143
splanchnic layer of lateral plate mesoderm1.94e-1384
somite2.38e-1383
paraxial mesoderm2.38e-1383
presomitic mesoderm2.38e-1383
presumptive segmental plate2.38e-1383
trunk paraxial mesoderm2.38e-1383
presumptive paraxial mesoderm2.38e-1383
mesenchyme2.57e-13238
entire embryonic mesenchyme2.57e-13238
multilaminar epithelium3.92e-1382
muscle tissue3.13e-1263
musculature3.13e-1263
musculature of body3.13e-1263
anatomical system3.86e-12625
surface structure3.93e-1295
skeletal muscle tissue4.17e-1261
striated muscle tissue4.17e-1261
myotome4.17e-1261
dermomyotome5.89e-1270
multi-tissue structure7.73e-12347
anatomical group8.11e-12626
epithelial tube8.16e-12118
vasculature7.22e-1179
vascular system7.22e-1179
unilaminar epithelium1.79e-10138
vessel1.00e-0969
integument1.23e-0945
integumental system1.23e-0945
blood vessel3.18e-0960
epithelial tube open at both ends3.18e-0960
blood vasculature3.18e-0960
vascular cord3.18e-0960
circulatory system5.83e-09113
artery5.95e-0942
arterial blood vessel5.95e-0942
arterial system5.95e-0942
cell layer6.67e-09312
epithelium6.96e-09309
primary circulatory organ8.42e-0927
systemic artery2.13e-0833
systemic arterial system2.13e-0833
cardiovascular system2.22e-08110
heart3.98e-0824
primitive heart tube3.98e-0824
primary heart field3.98e-0824
anterior lateral plate mesoderm3.98e-0824
heart tube3.98e-0824
heart primordium3.98e-0824
cardiac mesoderm3.98e-0824
cardiogenic plate3.98e-0824
heart rudiment3.98e-0824
skin of body4.21e-0840
mesoderm9.61e-08448
mesoderm-derived structure9.61e-08448
presumptive mesoderm9.61e-08448
compound organ3.91e-0769
anatomical cluster4.21e-07286
adipose tissue6.54e-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
E2F1#186934.907389214879320.008460985347239390.0327025960800982
NR3C1#290829.982015554115360.01278474365547170.0460676870905951
SMARCB1#6598318.25271578115740.000164397760679890.00203671859165445
SMC3#9126210.02995522995520.0126656379767470.0457774973924931



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.