Coexpression cluster:C2242

Full id: C2242_Mammary_Keratinocyte_Trabecular_Nucleus_salivary_Prostate_Skeletal

Phase1 CAGE Peaks

Hg19::chr12:76424402..76424485,+	p@chr12:76424402..76424485 +
Hg19::chr12:76424486..76424575,+	p@chr12:76424486..76424575 +
Hg19::chr12:76424595..76424611,+	p@chr12:76424595..76424611 +
Hg19::chr12:76424717..76424755,+	p@chr12:76424717..76424755 +

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
embryonic cell	7.24e-19	250
non-terminally differentiated cell	1.09e-09	106
somatic cell	3.02e-09	588
ectodermal cell	1.08e-08	72
epithelial cell	2.34e-08	253
contractile cell	3.65e-08	59
electrically responsive cell	5.38e-08	61
electrically active cell	5.38e-08	61
animal cell	1.12e-07	679
eukaryotic cell	1.12e-07	679
smooth muscle cell	1.37e-07	43
smooth muscle myoblast	1.37e-07	43
muscle precursor cell	2.87e-07	58
myoblast	2.87e-07	58
multi-potent skeletal muscle stem cell	2.87e-07	58
vascular associated smooth muscle cell	3.34e-07	32
muscle cell	5.03e-07	55

Uber Anatomy

Ontology term	p-value	n
anatomical system	1.18e-18	624
anatomical group	2.77e-18	625
multi-cellular organism	3.59e-17	656
embryo	9.58e-17	592
developing anatomical structure	9.95e-16	581
cell layer	1.27e-14	309
epithelium	2.85e-14	306
embryonic structure	4.27e-14	564
germ layer	1.73e-13	560
germ layer / neural crest	1.73e-13	560
embryonic tissue	1.73e-13	560
presumptive structure	1.73e-13	560
germ layer / neural crest derived structure	1.73e-13	560
epiblast (generic)	1.73e-13	560
organism subdivision	7.14e-13	264
multi-tissue structure	4.50e-12	342
anatomical cluster	5.92e-12	373
surface structure	2.31e-10	99
multilaminar epithelium	2.59e-10	83
epithelial tube	7.59e-10	117
anatomical conduit	2.30e-09	240
head	2.63e-09	56
unilaminar epithelium	2.86e-09	148
artery	1.63e-08	42
arterial blood vessel	1.63e-08	42
arterial system	1.63e-08	42
epithelial vesicle	2.07e-08	78
vasculature	2.49e-08	78
vascular system	2.49e-08	78
subdivision of head	2.91e-08	49
mesenchyme	6.23e-08	160
entire embryonic mesenchyme	6.23e-08	160
organ	7.02e-08	503
dense mesenchyme tissue	7.90e-08	73
somite	1.02e-07	71
presomitic mesoderm	1.02e-07	71
presumptive segmental plate	1.02e-07	71
dermomyotome	1.02e-07	71
trunk paraxial mesoderm	1.02e-07	71
paraxial mesoderm	1.20e-07	72
presumptive paraxial mesoderm	1.20e-07	72
anterior region of body	1.48e-07	62
craniocervical region	1.48e-07	62
systemic artery	1.64e-07	33
systemic arterial system	1.64e-07	33
trunk mesenchyme	1.80e-07	122
trunk	6.72e-07	199

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
EBF1#1879	3	6.67985013492675	0.00518429411827891	0.0240406044498238
SMARCB1#6598	3	13.6895368358681	0.000630578340937934	0.00518028564062116
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321516491580658

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.