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
mesodermal cell	1.01e-13	121
fibroblast	2.15e-10	76
endothelial cell of vascular tree	5.42e-09	24
endothelial cell	1.04e-08	36
lining cell	1.18e-08	58
barrier cell	1.18e-08	58
meso-epithelial cell	3.72e-08	45
non-terminally differentiated cell	1.35e-07	106
embryonic cell	8.04e-07	250

Uber Anatomy

Ontology term	p-value	n
anatomical cluster	5.61e-32	373
anatomical conduit	1.90e-28	240
tube	3.45e-26	192
cell layer	1.60e-25	309
epithelium	1.35e-24	306
structure with developmental contribution from neural crest	6.04e-23	132
neural plate	8.11e-22	82
presumptive neural plate	8.11e-22	82
neural tube	3.37e-20	56
neural rod	3.37e-20	56
future spinal cord	3.37e-20	56
neural keel	3.37e-20	56
multi-tissue structure	9.00e-20	342
neurectoderm	5.10e-19	86
regional part of nervous system	7.10e-19	53
regional part of brain	7.10e-19	53
central nervous system	8.57e-19	81
nervous system	1.80e-18	89
ectoderm-derived structure	8.86e-17	171
ectoderm	8.86e-17	171
presumptive ectoderm	8.86e-17	171
brain	1.36e-16	68
future brain	1.36e-16	68
ecto-epithelium	9.43e-16	104
vasculature	1.79e-15	78
vascular system	1.79e-15	78
pre-chordal neural plate	3.21e-15	61
multi-cellular organism	5.05e-15	656
anatomical system	8.37e-15	624
anatomical group	1.61e-14	625
regional part of forebrain	2.34e-14	41
forebrain	2.34e-14	41
anterior neural tube	2.34e-14	41
future forebrain	2.34e-14	41
brain grey matter	1.16e-13	34
gray matter	1.16e-13	34
vessel	1.41e-13	68
telencephalon	1.60e-13	34
cerebral hemisphere	2.68e-13	32
organ part	2.79e-13	218
epithelial tube	5.86e-13	117
regional part of telencephalon	8.07e-13	32
splanchnic layer of lateral plate mesoderm	1.39e-12	83
epithelial tube open at both ends	1.02e-11	59
blood vessel	1.02e-11	59
blood vasculature	1.02e-11	59
vascular cord	1.02e-11	59
developing anatomical structure	1.93e-11	581
cerebral cortex	1.85e-10	25
pallium	1.85e-10	25
germ layer	2.09e-10	560
germ layer / neural crest	2.09e-10	560
embryonic tissue	2.09e-10	560
presumptive structure	2.09e-10	560
germ layer / neural crest derived structure	2.09e-10	560
epiblast (generic)	2.09e-10	560
embryo	2.66e-10	592
circulatory system	3.78e-10	112
embryonic structure	6.11e-10	564
adult organism	6.23e-10	114
cardiovascular system	6.64e-10	109
regional part of cerebral cortex	3.11e-09	22
neocortex	4.06e-09	20
organ system subdivision	9.91e-09	223
artery	1.29e-08	42
arterial blood vessel	1.29e-08	42
arterial system	1.29e-08	42
systemic artery	5.88e-08	33
systemic arterial system	5.88e-08	33
simple squamous epithelium	1.19e-07	22
posterior neural tube	3.79e-07	15
chordal neural plate	3.79e-07	15
epithelial vesicle	5.06e-07	78

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.