Coexpression cluster:C3129

Full id: C3129_Melanocyte_melanoma_occipital_brain_parietal_aorta_Fibroblast

Phase1 CAGE Peaks

Hg19::chr11:19734342..19734353,+	p@chr11:19734342..19734353 +
Hg19::chr11:19734369..19734391,+	p1@NAV2
Hg19::chr11:19734399..19734410,+	p4@NAV2

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
non-terminally differentiated cell	4.14e-18	180
mesodermal cell	3.17e-12	119
fibroblast	3.53e-11	75
endothelial cell of vascular tree	5.59e-08	24
lining cell	2.28e-07	57
barrier cell	2.28e-07	57
endothelial cell	2.85e-07	35
meso-epithelial cell	8.75e-07	44

Uber Anatomy

Ontology term	p-value	n
anatomical cluster	3.01e-30	286
anatomical conduit	3.04e-28	241
tube	2.21e-26	194
cell layer	1.92e-25	312
epithelium	1.68e-24	309
neural plate	1.88e-21	86
presumptive neural plate	1.88e-21	86
neural tube	6.46e-21	57
neural rod	6.46e-21	57
future spinal cord	6.46e-21	57
neural keel	6.46e-21	57
regional part of nervous system	6.95e-20	94
nervous system	6.95e-20	94
regional part of brain	8.90e-19	59
neurectoderm	9.10e-19	90
central nervous system	9.25e-19	82
ectoderm-derived structure	3.02e-18	169
organism subdivision	3.24e-18	365
multi-cellular organism	4.19e-17	659
multi-tissue structure	1.18e-16	347
ectoderm	1.33e-16	173
presumptive ectoderm	1.33e-16	173
anatomical system	1.34e-16	625
brain	2.03e-16	69
future brain	2.03e-16	69
anatomical group	2.36e-16	626
pre-chordal neural plate	6.36e-16	61
head	4.14e-15	123
anterior neural tube	7.06e-15	42
regional part of forebrain	9.96e-15	41
forebrain	9.96e-15	41
future forebrain	9.96e-15	41
vasculature	2.68e-14	79
vascular system	2.68e-14	79
gray matter	3.35e-14	34
brain grey matter	3.35e-14	34
telencephalon	5.70e-14	34
regional part of telencephalon	1.52e-13	33
cerebral hemisphere	1.62e-13	32
organ part	1.62e-13	219
anterior region of body	1.65e-13	129
craniocervical region	1.65e-13	129
epithelial tube	7.01e-13	118
vessel	8.87e-13	69
splanchnic layer of lateral plate mesoderm	9.05e-12	84
embryonic structure	5.10e-11	605
developing anatomical structure	5.10e-11	605
adult organism	6.10e-11	115
cerebral cortex	7.07e-11	25
pallium	7.07e-11	25
germ layer	8.94e-11	604
embryonic tissue	8.94e-11	604
presumptive structure	8.94e-11	604
epiblast (generic)	8.94e-11	604
blood vessel	1.21e-10	60
epithelial tube open at both ends	1.21e-10	60
blood vasculature	1.21e-10	60
vascular cord	1.21e-10	60
embryo	1.82e-10	612
circulatory system	2.36e-10	113
cardiovascular system	4.70e-10	110
regional part of cerebral cortex	1.56e-09	22
neocortex	3.45e-09	20
artery	4.11e-08	42
arterial blood vessel	4.11e-08	42
arterial system	4.11e-08	42
organ	2.14e-07	511
posterior neural tube	2.46e-07	15
chordal neural plate	2.46e-07	15
systemic artery	2.68e-07	33
systemic arterial system	2.68e-07	33

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	6.33620157696263	0.00393075003576489	0.018918138386417
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323671971239271
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00435537729967659
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320472994850992
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00894939448785494
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127631460058241
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00718227983808478
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00199055067740732
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00244992681253872
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00136060702075187
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245469928933593
SUZ12#23512	3	50.1157809110629	7.93834897779404e-06	0.000221263204935103
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00611757484903337
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189562742835501
YY1#7528	3	4.91117074985386	0.00844145534180826	0.032799477452402

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.