Coexpression cluster:C2930

Full id: C2930_Eosinophils_Neutrophils_CD14_Whole_aorta_bladder_colon

Phase1 CAGE Peaks

Hg19::chr8:9008131..9008144,-	p3@PPP1R3B
Hg19::chr8:9008147..9008153,-	p6@PPP1R3B
Hg19::chr8:9008160..9008180,-	p1@PPP1R3B
Hg19::chr8:9008184..9008198,-	p2@PPP1R3B

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
endothelial cell of vascular tree	3.62e-09	24
endothelial cell	3.15e-07	36

Uber Anatomy

Ontology term	p-value	n
circulatory system	2.00e-14	112
lateral plate mesoderm	1.79e-13	203
cardiovascular system	3.02e-13	109
mesoderm	3.25e-13	315
mesoderm-derived structure	3.25e-13	315
presumptive mesoderm	3.25e-13	315
multi-cellular organism	5.59e-12	656
vessel	1.72e-10	68
splanchnic layer of lateral plate mesoderm	2.29e-10	83
epithelial tube	4.59e-10	117
vasculature	4.60e-10	78
vascular system	4.60e-10	78
epithelial tube open at both ends	1.17e-09	59
blood vessel	1.17e-09	59
blood vasculature	1.17e-09	59
vascular cord	1.17e-09	59
embryo	3.15e-07	592
developing anatomical structure	6.94e-07	581

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
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00513877704630931
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.00820463206288372
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00999739356028686
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0161327520855575
GATA1#2623	4	13.5603081438004	2.95627390049268e-05	0.000615530880968012
GATA2#2624	4	12.744931733554	3.78864877853583e-05	0.000725091973211479
GATA3#2625	4	27.236516357206	1.81561517799785e-06	6.79888969433191e-05
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186703062661127
HMGN3#9324	4	8.17854772335059	0.000223457028444047	0.00248669457577708
IRF1#3659	4	7.6371637535639	0.000293885399618549	0.00308163627015679
MEF2A#4205	4	18.7432309096441	8.0978922767748e-06	0.000224869920631237
NANOG#79923	4	29.2447784810127	1.36586687657858e-06	5.35070407813168e-05
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.0076952082696044
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.0044505918991875
RAD21#5885	4	10.3550338954563	8.6948481184721e-05	0.00130134887166109
SMC3#9126	4	15.0449328449328	1.95092670935632e-05	0.000439880903709984
STAT1#6772	4	20.7065874971992	5.43610708103893e-06	0.000165715583022949
STAT3#6774	4	10.5194649971542	8.16377768286615e-05	0.00123603475996065
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0323481888170968
TAF7#6879	4	11.4330694049239	5.85061525419808e-05	0.000972362200084649
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0245157294064735
TFAP2C#7022	4	10.8092286098602	7.32289634782688e-05	0.00114955053610505
YY1#7528	4	4.91117074985386	0.0017187183805544	0.010712014617576
ZNF143#7702	4	13.5008765522279	3.00867915035614e-05	0.000622471160427981
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00250163212467819

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.