Coexpression cluster:C3330

Full id: C3330_Hepatocyte_liver_Mesenchymal_tenocyte_Synoviocyte_Fibroblast_Nucleus

Phase1 CAGE Peaks

Hg19::chr12:7245125..7245138,-	p3@C1R
Hg19::chr12:7245139..7245150,-	p4@C1R
Hg19::chr12:7245152..7245169,-	p5@C1R

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

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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

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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>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	1.43e-24	180
fibroblast	3.00e-14	75
contractile cell	5.07e-10	59
muscle precursor cell	6.08e-10	57
myoblast	6.08e-10	57
multi-potent skeletal muscle stem cell	6.08e-10	57
muscle cell	2.82e-09	54
electrically responsive cell	9.50e-08	60
electrically active cell	9.50e-08	60

Uber Anatomy

Ontology term	p-value	n
organism subdivision	2.72e-21	365
multi-tissue structure	7.40e-20	347
trunk mesenchyme	8.59e-13	143
anatomical cluster	2.62e-12	286
mesenchyme	7.92e-12	238
entire embryonic mesenchyme	7.92e-12	238
multi-cellular organism	1.01e-11	659
trunk	4.52e-11	216
muscle tissue	1.28e-10	63
musculature	1.28e-10	63
musculature of body	1.28e-10	63
cell layer	1.82e-10	312
epithelium	2.10e-10	309
somite	2.16e-10	83
paraxial mesoderm	2.16e-10	83
presomitic mesoderm	2.16e-10	83
presumptive segmental plate	2.16e-10	83
trunk paraxial mesoderm	2.16e-10	83
presumptive paraxial mesoderm	2.16e-10	83
skeletal muscle tissue	3.18e-10	61
striated muscle tissue	3.18e-10	61
myotome	3.18e-10	61
dermomyotome	2.92e-09	70
multilaminar epithelium	5.26e-09	82
anatomical system	3.43e-08	625
surface structure	4.03e-08	95
anatomical group	4.23e-08	626
anatomical conduit	5.35e-08	241
unilaminar epithelium	2.42e-07	138
primary circulatory organ	4.90e-07	27
primordium	5.93e-07	168

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

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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

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115031311017229
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0278697564262118
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171386089342465
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00880520110521641
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00662485215589672
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00308403410861212
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00641663693256112
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328373493162661
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00388176093248981

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

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This analysis result is provided for C0 - C305 clusters.