Coexpression cluster:C2670

Full id: C2670_uterus_lung_cervix_adipose_penis_ductus_seminal

Phase1 CAGE Peaks

Hg19::chr2:173686542..173686585,+	p5@RAPGEF4
Hg19::chr5:38557323..38557328,-	p12@LIFR
Hg19::chr5:38557343..38557361,-	p4@LIFR
Hg19::chr5:38557372..38557385,-	p5@LIFR

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:0004923	leukemia inhibitory factor receptor activity	0.0046508889673849
GO:0030552	cAMP binding	0.022470032592992
GO:0016208	AMP binding	0.022470032592992
GO:0005952	cAMP-dependent protein kinase complex	0.022470032592992
GO:0030551	cyclic nucleotide binding	0.022470032592992
GO:0008603	cAMP-dependent protein kinase regulator activity	0.022470032592992
GO:0004896	hematopoietin/interferon-class (D200-domain) cytokine receptor activity	0.0457985933512357

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	7.56e-15	24
endothelial cell	2.22e-11	35
blood vessel endothelial cell	4.98e-11	18
embryonic blood vessel endothelial progenitor cell	4.98e-11	18
meso-epithelial cell	3.01e-09	44

Uber Anatomy

Ontology term	p-value	n
adult organism	6.05e-62	115
anatomical conduit	1.59e-28	241
anatomical cluster	2.07e-28	286
neural tube	1.29e-26	57
neural rod	1.29e-26	57
future spinal cord	1.29e-26	57
neural keel	1.29e-26	57
tube	2.41e-25	194
regional part of brain	4.72e-23	59
anterior neural tube	7.49e-22	42
regional part of forebrain	5.66e-21	41
forebrain	5.66e-21	41
future forebrain	5.66e-21	41
central nervous system	1.17e-20	82
regional part of nervous system	4.25e-19	94
nervous system	4.25e-19	94
neural plate	1.67e-18	86
presumptive neural plate	1.67e-18	86
brain	1.88e-18	69
future brain	1.88e-18	69
gray matter	9.48e-18	34
brain grey matter	9.48e-18	34
neurectoderm	1.36e-17	90
telencephalon	1.55e-17	34
regional part of telencephalon	6.60e-17	33
cerebral hemisphere	1.89e-16	32
regional part of cerebral cortex	6.37e-14	22
cell layer	1.24e-13	312
epithelium	2.08e-13	309
neocortex	9.83e-13	20
cerebral cortex	1.97e-12	25
pallium	1.97e-12	25
pre-chordal neural plate	2.93e-12	61
endothelium	4.98e-11	18
blood vessel endothelium	4.98e-11	18
cardiovascular system endothelium	4.98e-11	18
multi-cellular organism	3.27e-10	659
anatomical group	3.46e-10	626
anterior region of body	5.74e-10	129
craniocervical region	5.74e-10	129
anatomical system	6.94e-10	625
multi-tissue structure	1.95e-09	347
head	6.98e-09	123
ectoderm-derived structure	1.11e-08	169
ectoderm	1.97e-08	173
presumptive ectoderm	1.97e-08	173
embryo	4.30e-08	612
simple squamous epithelium	6.42e-08	22
vessel	9.13e-08	69
embryonic structure	2.19e-07	605
developing anatomical structure	2.19e-07	605
splanchnic layer of lateral plate mesoderm	2.22e-07	84
brainstem	3.66e-07	8
squamous epithelium	4.44e-07	25
germ layer	4.74e-07	604
embryonic tissue	4.74e-07	604
presumptive structure	4.74e-07	604
epiblast (generic)	4.74e-07	604
nucleus of brain	6.76e-07	9
neural nucleus	6.76e-07	9
circulatory system	8.95e-07	113

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)
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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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No analysis results for this cluster

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.