Coexpression cluster:C3132

Full id: C3132_Pericytes_Mesenchymal_Skeletal_skeletal_amniotic_Hair_gastric

Phase1 CAGE Peaks

Hg19::chr11:2158507..2158526,-	p3@IGF2
Hg19::chr17:48277566..48277608,-	p5@COL1A1
Hg19::chr1:168409732..168409736,+	p@chr1:168409732..168409736 +

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:0001501	skeletal development	0.0030134928219141
GO:0005584	collagen type I	0.0062794040249056
GO:0008147	structural constituent of bone	0.0062794040249056
GO:0006349	genetic imprinting	0.0064749681926325
GO:0018445	prothoracicotrophic hormone activity	0.0064749681926325
GO:0005583	fibrillar collagen	0.0064749681926325
GO:0005159	insulin-like growth factor receptor binding	0.0064749681926325
GO:0051591	response to cAMP	0.0064749681926325
GO:0031960	response to corticosteroid stimulus	0.00680178652952636
GO:0009612	response to mechanical stimulus	0.00784740648934456
GO:0048513	organ development	0.00784740648934456
GO:0042542	response to hydrogen peroxide	0.00784740648934456
GO:0043434	response to peptide hormone stimulus	0.00796790119733836
GO:0000302	response to reactive oxygen species	0.00907963454196166
GO:0008286	insulin receptor signaling pathway	0.00970930687956354
GO:0005184	neuropeptide hormone activity	0.00970930687956354
GO:0048545	response to steroid hormone stimulus	0.00988452957792736
GO:0048731	system development	0.00988452957792736
GO:0007584	response to nutrient	0.00988452957792736
GO:0010035	response to inorganic substance	0.00988452957792736
GO:0005581	collagen	0.0119441092498285
GO:0048856	anatomical structure development	0.0119441092498285
GO:0031667	response to nutrient levels	0.0119441092498285
GO:0010033	response to organic substance	0.0119441092498285
GO:0040029	regulation of gene expression, epigenetic	0.0119441092498285
GO:0009991	response to extracellular stimulus	0.0119441092498285
GO:0009725	response to hormone stimulus	0.0130795109121471
GO:0007275	multicellular organismal development	0.0130795109121471
GO:0031214	biomineral formation	0.0137976083286762
GO:0001503	ossification	0.0137976083286762
GO:0046849	bone remodeling	0.014564672669458
GO:0048771	tissue remodeling	0.0154302476562255
GO:0006979	response to oxidative stress	0.0166990454661848
GO:0005201	extracellular matrix structural constituent	0.0166990454661848
GO:0044420	extracellular matrix part	0.0166990454661848
GO:0050954	sensory perception of mechanical stimulus	0.0166990454661848
GO:0007605	sensory perception of sound	0.0166990454661848
GO:0008544	epidermis development	0.0166990454661848
GO:0006817	phosphate transport	0.0171539397978626
GO:0007398	ectoderm development	0.0171539397978626
GO:0009628	response to abiotic stimulus	0.0184838697208335
GO:0032502	developmental process	0.0184838697208335
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.0226393100151102
GO:0032501	multicellular organismal process	0.0226393100151102
GO:0005179	hormone activity	0.0226393100151102
GO:0008083	growth factor activity	0.0258076074285635
GO:0015698	inorganic anion transport	0.0259546771181936
GO:0007167	enzyme linked receptor protein signaling pathway	0.029184688142699
GO:0009888	tissue development	0.029184688142699
GO:0006820	anion transport	0.0302808613505519
GO:0005578	proteinaceous extracellular matrix	0.038638277528768
GO:0009719	response to endogenous stimulus	0.0475404146506583

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	2.84e-12	180
fibroblast	1.84e-07	75
contractile cell	2.87e-07	59

Uber Anatomy

Ontology term	p-value	n
multi-tissue structure	1.61e-23	347
organism subdivision	1.97e-21	365
multi-cellular organism	1.18e-16	659
cell layer	1.42e-16	312
epithelium	1.62e-15	309
trunk	3.51e-14	216
anatomical cluster	4.32e-14	286
trunk mesenchyme	7.48e-14	143
mesenchyme	3.64e-13	238
entire embryonic mesenchyme	3.64e-13	238
anatomical system	2.19e-11	625
embryo	2.43e-11	612
organ part	4.26e-11	219
anatomical group	4.36e-11	626
organ	1.33e-10	511
embryonic structure	1.83e-10	605
developing anatomical structure	1.83e-10	605
endoderm-derived structure	2.15e-10	169
endoderm	2.15e-10	169
presumptive endoderm	2.15e-10	169
germ layer	4.05e-10	604
embryonic tissue	4.05e-10	604
presumptive structure	4.05e-10	604
epiblast (generic)	4.05e-10	604
anatomical conduit	4.21e-10	241
unilaminar epithelium	1.25e-09	138
extraembryonic membrane	3.30e-09	14
membranous layer	3.30e-09	14
extraembryonic structure	1.80e-08	24
compound organ	2.91e-08	69
tube	6.49e-08	194
muscle tissue	9.24e-08	63
musculature	9.24e-08	63
musculature of body	9.24e-08	63
skeletal muscle tissue	1.31e-07	61
striated muscle tissue	1.31e-07	61
myotome	1.31e-07	61
epithelial tube	1.59e-07	118
digestive system	1.67e-07	155
digestive tract	1.67e-07	155
primitive gut	1.67e-07	155
organ component layer	5.52e-07	57
immaterial anatomical entity	6.74e-07	126
somite	6.88e-07	83
paraxial mesoderm	6.88e-07	83
presomitic mesoderm	6.88e-07	83
presumptive segmental plate	6.88e-07	83
trunk paraxial mesoderm	6.88e-07	83
presumptive paraxial mesoderm	6.88e-07	83
abdominal segment of trunk	7.62e-07	61
abdomen	7.62e-07	61

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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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.