Coexpression cluster:C2471

Full id: C2471_basal_Smooth_mucinous_Chondrocyte_H9_Cardiac_Sertoli

Phase1 CAGE Peaks

Hg19::chr19:10217364..10217409,+	p3@PPAN-P2RY11 p3@PPAN
Hg19::chr5:176943586..176943600,-	p5@DDX41
Hg19::chr5:176943608..176943623,-	p4@DDX41
Hg19::chr5:176943630..176943646,-	p7@DDX41

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	1.57e-16	180
animal cell	5.14e-12	679
eukaryotic cell	5.14e-12	679
somatic cell	2.74e-10	591
vascular associated smooth muscle cell	4.18e-10	32
smooth muscle cell	5.46e-09	42
smooth muscle myoblast	5.46e-09	42
muscle precursor cell	6.33e-09	57
myoblast	6.33e-09	57
multi-potent skeletal muscle stem cell	6.33e-09	57
embryonic cell	1.81e-08	248
electrically responsive cell	2.73e-08	60
electrically active cell	2.73e-08	60
contractile cell	3.36e-08	59
muscle cell	7.56e-08	54
mesodermal cell	1.09e-07	119
native cell	4.04e-07	722

Uber Anatomy

Ontology term	p-value	n
artery	2.19e-10	42
arterial blood vessel	2.19e-10	42
arterial system	2.19e-10	42
systemic artery	1.04e-08	33
systemic arterial system	1.04e-08	33
vessel	6.63e-08	69
skeletal muscle tissue	1.62e-07	61
striated muscle tissue	1.62e-07	61
myotome	1.62e-07	61
vasculature	1.63e-07	79
vascular system	1.63e-07	79
blood vessel	8.62e-07	60
epithelial tube open at both ends	8.62e-07	60
blood vasculature	8.62e-07	60
vascular cord	8.62e-07	60

Disease

Ontology term	p-value	n
ovarian cancer	3.45e-07	14

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
ELK4#2005	4	16.235681658468	1.43847748454449e-05	0.000343311585942281
ETS1#2113	4	9.72876092220234	0.000111595531741814	0.00154554114037704
GABPB1#2553	4	7.06768383618217	0.000400687686442317	0.00390331324357328
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186029620194955
JUND#3727	3	5.24599795640327	0.0104343275174842	0.0386902908328671
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00887641960756713
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.00767980655847704
NFYA#4800	3	13.8191855248729	0.000613241180673451	0.00508748079024184
NFYB#4801	3	12.5698449401523	0.00081145639769735	0.00618912544505321
NR2C2#7182	3	24.4609581789307	0.000112590606343803	0.00155560925200958
NRF1#4899	4	12.2102794477109	4.49717228915276e-05	0.000793780930719664
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00796258684930302
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322197933084972
TAF7#6879	4	11.4330694049239	5.85061525419808e-05	0.000968816246286972
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244194067896107
TRIM28#10155	3	13.9428937839469	0.000597285818425842	0.00499399036030554
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106858690883868
ZBTB7A#51341	3	5.51393198090692	0.00903835282108109	0.0342422653999669

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.