Coexpression cluster:C1346

Full id: C1346_Endothelial_Renal_Hepatic_Lymphatic_heart_breast_adipose

Phase1 CAGE Peaks

Hg19::chr11:62344721..62344758,-	p2@TUT1
Hg19::chr12:120687909..120687930,-	p13@PXN
Hg19::chr12:120687948..120687971,-	p6@PXN
Hg19::chrX:45060073..45060131,-	p1@CXorf36
Hg19::chrX:45060135..45060149,-	p2@CXorf36
Hg19::chrX:45060204..45060209,-	p5@CXorf36

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:0050265	RNA uridylyltransferase activity	0.00512186506534793
GO:0017166	vinculin binding	0.0128031549908582
GO:0007172	signal complex assembly	0.0273045536036868

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	7.18e-20	24
endothelial cell	4.27e-17	35
blood vessel endothelial cell	5.77e-15	18
embryonic blood vessel endothelial progenitor cell	5.77e-15	18
meso-epithelial cell	1.88e-14	44
lining cell	1.68e-08	57
barrier cell	1.68e-08	57
endothelial cell of artery	8.45e-08	9

Uber Anatomy

Ontology term	p-value	n
adult organism	1.94e-45	115
anatomical conduit	3.29e-27	241
anatomical cluster	4.94e-24	286
tube	9.26e-21	194
neural tube	9.10e-20	57
neural rod	9.10e-20	57
future spinal cord	9.10e-20	57
neural keel	9.10e-20	57
cell layer	2.64e-17	312
epithelium	3.88e-17	309
anterior neural tube	5.27e-16	42
regional part of brain	9.04e-16	59
anatomical system	1.56e-15	625
anatomical group	2.34e-15	626
regional part of forebrain	2.64e-15	41
forebrain	2.64e-15	41
future forebrain	2.64e-15	41
multi-cellular organism	4.38e-15	659
central nervous system	5.56e-15	82
endothelium	5.77e-15	18
blood vessel endothelium	5.77e-15	18
cardiovascular system endothelium	5.77e-15	18
neural plate	1.68e-14	86
presumptive neural plate	1.68e-14	86
brain	3.48e-14	69
future brain	3.48e-14	69
neurectoderm	2.57e-13	90
gray matter	1.86e-12	34
brain grey matter	1.86e-12	34
telencephalon	2.70e-12	34
regional part of telencephalon	6.68e-12	33
simple squamous epithelium	1.02e-11	22
regional part of nervous system	1.68e-11	94
nervous system	1.68e-11	94
cerebral hemisphere	1.73e-11	32
regional part of cerebral cortex	6.94e-11	22
organism subdivision	2.88e-10	365
squamous epithelium	5.69e-10	25
multi-tissue structure	5.74e-10	347
neocortex	6.23e-10	20
splanchnic layer of lateral plate mesoderm	1.24e-09	84
vessel	1.62e-09	69
embryo	3.47e-09	612
organ part	3.70e-09	219
organ	4.75e-09	511
embryonic structure	5.46e-09	605
developing anatomical structure	5.46e-09	605
anterior region of body	6.25e-09	129
craniocervical region	6.25e-09	129
pre-chordal neural plate	6.85e-09	61
germ layer	1.13e-08	604
embryonic tissue	1.13e-08	604
presumptive structure	1.13e-08	604
epiblast (generic)	1.13e-08	604
cerebral cortex	1.33e-08	25
pallium	1.33e-08	25
ectoderm-derived structure	2.04e-08	169
compound organ	2.19e-08	69
head	6.15e-08	123
ectoderm	6.51e-08	173
presumptive ectoderm	6.51e-08	173
endothelial tube	8.45e-08	9
arterial system endothelium	8.45e-08	9
endothelium of artery	8.45e-08	9
lymphoid system	9.76e-08	10
vasculature	1.37e-07	79
vascular system	1.37e-07	79
epithelial tube	5.40e-07	118

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
GATA2#2624	3	6.372465866777	0.00805882130874255	0.0318845034914484

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.