Coexpression cluster:C2678

Full id: C2678_lung_Endothelial_Lymphatic_mature_migratory_adipose_Mast

Phase1 CAGE Peaks

Hg19::chr2:188312865..188312876,-	p3@CALCRL
Hg19::chr2:188312971..188312987,-	p1@CALCRL
Hg19::chr2:188312993..188313033,-	p2@CALCRL
Hg19::chr4:101439242..101439256,-	p5@EMCN

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:0001635	calcitonin gene-related polypeptide receptor activity	0.00276698457553279
GO:0004948	calcitonin receptor activity	0.00553372479694806
GO:0048661	positive regulation of smooth muscle cell proliferation	0.00737786532194403
GO:0048660	regulation of smooth muscle cell proliferation	0.00774607439651214
GO:0048659	smooth muscle cell proliferation	0.00774607439651214
GO:0033002	muscle cell proliferation	0.00922070262497986
GO:0007189	G-protein signaling, adenylate cyclase activating pathway	0.0138269813688443
GO:0001633	secretin-like receptor activity	0.0138269813688443
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.023612775104622
GO:0019933	cAMP-mediated signaling	0.023612775104622
GO:0007507	heart development	0.023612775104622
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.0259208404334235
GO:0019935	cyclic-nucleotide-mediated signaling	0.0259208404334235
GO:0005886	plasma membrane	0.0423490121090567
GO:0008284	positive regulation of cell proliferation	0.0428337292268629
GO:0019932	second-messenger-mediated signaling	0.0461648561898207

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	9.06e-16	36
endothelial cell of vascular tree	1.16e-15	24
blood vessel endothelial cell	1.11e-11	18
embryonic blood vessel endothelial progenitor cell	1.11e-11	18
meso-epithelial cell	4.43e-10	45

Uber Anatomy

Ontology term	p-value	n
adult organism	4.84e-31	114
embryonic structure	6.82e-17	564
germ layer	1.41e-16	560
germ layer / neural crest	1.41e-16	560
embryonic tissue	1.41e-16	560
presumptive structure	1.41e-16	560
germ layer / neural crest derived structure	1.41e-16	560
epiblast (generic)	1.41e-16	560
anatomical conduit	3.62e-16	240
multi-cellular organism	4.72e-16	656
developing anatomical structure	1.12e-15	581
tube	1.27e-15	192
embryo	2.57e-15	592
neural tube	3.32e-15	56
neural rod	3.32e-15	56
future spinal cord	3.32e-15	56
neural keel	3.32e-15	56
circulatory system	6.90e-14	112
anatomical system	9.33e-14	624
regional part of nervous system	1.59e-13	53
regional part of brain	1.59e-13	53
anatomical group	1.99e-13	625
lateral plate mesoderm	2.05e-13	203
central nervous system	2.34e-13	81
cardiovascular system	4.21e-13	109
vasculature	1.22e-12	78
vascular system	1.22e-12	78
structure with developmental contribution from neural crest	1.22e-12	132
mesoderm	1.24e-12	315
mesoderm-derived structure	1.24e-12	315
presumptive mesoderm	1.24e-12	315
splanchnic layer of lateral plate mesoderm	2.94e-12	83
brain	4.11e-12	68
future brain	4.11e-12	68
anatomical cluster	4.53e-12	373
vessel	5.06e-12	68
blood vessel endothelium	1.11e-11	18
endothelium	1.11e-11	18
cardiovascular system endothelium	1.11e-11	18
neurectoderm	1.47e-11	86
nervous system	1.80e-11	89
neural plate	4.84e-11	82
presumptive neural plate	4.84e-11	82
tissue	5.92e-11	773
epithelial tube open at both ends	2.90e-10	59
blood vessel	2.90e-10	59
blood vasculature	2.90e-10	59
vascular cord	2.90e-10	59
regional part of forebrain	3.92e-10	41
forebrain	3.92e-10	41
anterior neural tube	3.92e-10	41
future forebrain	3.92e-10	41
simple squamous epithelium	4.46e-09	22
brain grey matter	1.12e-08	34
gray matter	1.12e-08	34
cell layer	1.29e-08	309
telencephalon	2.35e-08	34
epithelium	3.21e-08	306
squamous epithelium	7.33e-08	25
regional part of telencephalon	7.52e-08	32
cerebral hemisphere	9.44e-08	32
ecto-epithelium	6.51e-07	104
primary circulatory organ	6.65e-07	27
regional part of cerebral cortex	7.70e-07	22
immune system	9.10e-07	93

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
FOS#2353	3	6.7484664816708	0.00503245277631794	0.0234730175296266
GATA2#2624	4	12.744931733554	3.78864877853583e-05	0.000722576131814288
JUN#3725	3	9.38462189425225	0.00191899450203047	0.0112873319890494
RAD21#5885	3	7.76627542159225	0.003341119385872	0.0172701394477152
SETDB1#9869	3	30.2400196335079	5.98509618524166e-05	0.000985149661923489
SMC3#9126	3	11.2836996336996	0.00111580236686805	0.00765759517632624
TRIM28#10155	3	13.9428937839469	0.000597285818425842	0.00499479010253635
WRNIP1#56897	3	82.3649732620321	2.99417904077464e-06	0.00010146303206991

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.