Coexpression cluster:C2744

Full id: C2744_breast_Renal_mature_adipose_lung_Endothelial_heart

Phase1 CAGE Peaks

Hg19::chr3:52479112..52479126,-	p1@SEMA3G
Hg19::chr7:1094939..1094950,+	p4@GPR146
Hg19::chr7:1094970..1094983,+	p5@GPR146
Hg19::chr7:1094987..1095014,+	p2@GPR146

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	6.91e-11	24
endothelial cell	1.67e-09	35
blood vessel endothelial cell	5.09e-08	18
embryonic blood vessel endothelial progenitor cell	5.09e-08	18

Uber Anatomy

Ontology term	p-value	n
adult organism	2.72e-56	115
neural tube	2.02e-19	57
neural rod	2.02e-19	57
future spinal cord	2.02e-19	57
neural keel	2.02e-19	57
anterior neural tube	4.70e-15	42
regional part of brain	9.88e-15	59
regional part of nervous system	1.70e-14	94
nervous system	1.70e-14	94
regional part of forebrain	2.14e-14	41
forebrain	2.14e-14	41
future forebrain	2.14e-14	41
central nervous system	2.74e-14	82
brain	6.97e-14	69
future brain	6.97e-14	69
neural plate	2.87e-12	86
presumptive neural plate	2.87e-12	86
gray matter	4.71e-12	34
brain grey matter	4.71e-12	34
neurectoderm	5.41e-12	90
telencephalon	6.14e-12	34
regional part of telencephalon	1.57e-11	33
cerebral hemisphere	5.84e-11	32
regional part of cerebral cortex	3.46e-10	22
anatomical conduit	7.42e-10	241
neocortex	2.08e-09	20
tube	6.80e-09	194
pre-chordal neural plate	2.66e-08	61
cerebral cortex	4.62e-08	25
pallium	4.62e-08	25
endothelium	5.09e-08	18
blood vessel endothelium	5.09e-08	18
cardiovascular system endothelium	5.09e-08	18
anatomical cluster	6.32e-07	286

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	3	4.75215118272197	0.0138620699668949	0.0487372740371161
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00998346455302453
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378767194514211
GATA1#2623	3	10.1702311078503	0.00151515816849827	0.00966715156452998
GATA2#2624	3	9.5586988001655	0.00181815161835744	0.0109048375851164
HMGN3#9324	3	6.13391079251294	0.00664069668332472	0.0283080702412143
NRF1#4899	3	9.15770958578318	0.00206195379173342	0.0119651290173823
TAL1#6886	3	22.4014625080802	0.000146275639593017	0.00188953389282067
TRIM28#10155	3	13.9428937839469	0.000597285818425842	0.0049955901009511

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.