Coexpression cluster:C1492

Full id: C1492_chorionic_amniotic_Smooth_basal_spindle_placenta_mesenchymal

Phase1 CAGE Peaks

Hg19::chr22:33197683..33197698,+	p1@TIMP3
Hg19::chr22:33253227..33253256,+	p@chr22:33253227..33253256 +
Hg19::chr22:33255260..33255310,-	p2@CU676956
Hg19::chr22:33255345..33255482,-	p1@CU676956
Hg19::chr22:33256226..33256238,-	p4@ENST00000327661
Hg19::chr22:33256911..33256925,+	p3@TIMP3

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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GO ID	GO name	FDR corrected p-value
GO:0008191	metalloendopeptidase inhibitor activity	0.00900741787354292
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.0227077761517889
GO:0050953	sensory perception of light stimulus	0.0227077761517889
GO:0007601	visual perception	0.0227077761517889
GO:0004866	endopeptidase inhibitor activity	0.0227077761517889
GO:0030414	protease inhibitor activity	0.0227077761517889
GO:0007167	enzyme linked receptor protein signaling pathway	0.0227077761517889
GO:0004857	enzyme inhibitor activity	0.0247851171553044
GO:0005578	proteinaceous extracellular matrix	0.0247851171553044
GO:0044421	extracellular region part	0.0457596095179988
GO:0007600	sensory perception	0.0457596095179988

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	2.27e-17	180
fibroblast	1.21e-11	75
preadipocyte	4.15e-08	12
muscle cell	4.21e-07	54
contractile cell	4.43e-07	59
smooth muscle cell	4.53e-07	42
smooth muscle myoblast	4.53e-07	42
vascular associated smooth muscle cell	7.82e-07	32
fat cell	8.15e-07	15

Uber Anatomy

Ontology term	p-value	n
organism subdivision	1.75e-15	365
multi-cellular organism	3.62e-13	659
organ component layer	2.29e-11	57
anatomical system	5.38e-11	625
anatomical group	1.02e-10	626
multi-tissue structure	1.10e-09	347
adult organism	2.79e-09	115
surface structure	8.71e-09	95
organ	1.62e-08	511
organ part	2.29e-08	219
anatomical cluster	4.23e-08	286
cell layer	6.81e-08	312
dermomyotome	9.36e-08	70
somite	1.01e-07	83
paraxial mesoderm	1.01e-07	83
presomitic mesoderm	1.01e-07	83
presumptive segmental plate	1.01e-07	83
trunk paraxial mesoderm	1.01e-07	83
presumptive paraxial mesoderm	1.01e-07	83
muscle tissue	1.48e-07	63
musculature	1.48e-07	63
musculature of body	1.48e-07	63
epithelium	1.87e-07	309
extraembryonic membrane	2.23e-07	14
membranous layer	2.23e-07	14
splanchnic layer of lateral plate mesoderm	2.43e-07	84
multilaminar epithelium	2.81e-07	82
skeletal muscle tissue	3.16e-07	61
striated muscle tissue	3.16e-07	61
myotome	3.16e-07	61
anatomical conduit	3.90e-07	241
integument	5.13e-07	45
integumental system	5.13e-07	45
trunk mesenchyme	5.61e-07	143

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)
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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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No analysis results for this cluster

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.