Coexpression cluster:C2257

Full id: C2257_gastric_Fibroblast_synovial_alveolar_osteosarcoma_Smooth_mesenchymal

Phase1 CAGE Peaks

Hg19::chr13:24153488..24153553,+	p1@TNFRSF19
Hg19::chr13:24153554..24153576,+	p4@TNFRSF19
Hg19::chr13:24153584..24153602,+	p5@TNFRSF19
Hg19::chr13:24153617..24153622,+	p11@TNFRSF19

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	1.60e-24	180
fibroblast	2.36e-13	75
skin fibroblast	1.76e-08	23

Uber Anatomy

Ontology term	p-value	n
organism subdivision	1.06e-21	365
multi-tissue structure	2.37e-17	347
surface structure	1.00e-11	95
trunk mesenchyme	1.69e-10	143
somite	2.24e-10	83
paraxial mesoderm	2.24e-10	83
presomitic mesoderm	2.24e-10	83
presumptive segmental plate	2.24e-10	83
trunk paraxial mesoderm	2.24e-10	83
presumptive paraxial mesoderm	2.24e-10	83
trunk	5.50e-09	216
cell layer	6.63e-09	312
mesenchyme	7.28e-09	238
entire embryonic mesenchyme	7.28e-09	238
epithelium	1.55e-08	309
organ	6.74e-08	511
dermomyotome	9.99e-08	70
head	1.23e-07	123
anterior region of body	1.46e-07	129
craniocervical region	1.46e-07	129
integument	2.13e-07	45
integumental system	2.13e-07	45
multi-cellular organism	2.91e-07	659
skin of body	2.96e-07	40
anatomical system	7.51e-07	625
anatomical group	8.66e-07	626

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
CHD2#1106	4	10.3440228341169	8.73193255208051e-05	0.0012895281445231
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101315585089166
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185685920579265
IRF1#3659	4	7.6371637535639	0.000293885399618549	0.00307023079431446
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00794961593177955
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321528855697393

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.