Coexpression cluster:C3263

Full id: C3263_testicular_uterus_large_heart_merkel_teratocarcinoma_spinal

Phase1 CAGE Peaks

Hg19::chr12:19282623..19282642,+	p3@PLEKHA5
Hg19::chr12:19282643..19282710,+	p1@PLEKHA5
Hg19::chr12:19282713..19282734,+	p5@PLEKHA5

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
central nervous system	1.59e-24	82
ectoderm-derived structure	1.20e-23	169
ectoderm	2.96e-23	173
presumptive ectoderm	2.96e-23	173
neural tube	1.15e-22	57
neural rod	1.15e-22	57
future spinal cord	1.15e-22	57
neural keel	1.15e-22	57
head	1.25e-22	123
adult organism	3.40e-22	115
anterior region of body	4.46e-22	129
craniocervical region	4.46e-22	129
regional part of brain	1.29e-21	59
brain	2.48e-21	69
future brain	2.48e-21	69
organ	6.91e-21	511
regional part of nervous system	1.09e-20	94
nervous system	1.09e-20	94
multi-tissue structure	3.52e-20	347
neural plate	3.62e-20	86
presumptive neural plate	3.62e-20	86
neurectoderm	1.98e-19	90
organism subdivision	3.47e-18	365
anterior neural tube	1.71e-17	42
regional part of forebrain	2.28e-17	41
forebrain	2.28e-17	41
future forebrain	2.28e-17	41
gray matter	2.16e-15	34
brain grey matter	2.16e-15	34
pre-chordal neural plate	2.17e-15	61
telencephalon	2.57e-15	34
regional part of telencephalon	6.22e-15	33
cerebral hemisphere	7.63e-15	32
cell layer	8.65e-14	312
anatomical conduit	1.59e-13	241
epithelium	1.77e-13	309
multi-cellular organism	2.98e-13	659
anatomical cluster	1.89e-12	286
organ part	2.82e-12	219
anatomical group	9.14e-12	626
anatomical system	9.33e-12	625
cerebral cortex	1.97e-11	25
pallium	1.97e-11	25
embryo	2.58e-11	612
regional part of cerebral cortex	5.09e-11	22
tube	1.10e-10	194
neocortex	2.82e-10	20
digestive system	1.12e-09	155
digestive tract	1.12e-09	155
primitive gut	1.12e-09	155
embryonic structure	4.06e-09	605
developing anatomical structure	4.06e-09	605
endoderm-derived structure	4.15e-09	169
endoderm	4.15e-09	169
presumptive endoderm	4.15e-09	169
germ layer	8.71e-09	604
embryonic tissue	8.71e-09	604
presumptive structure	8.71e-09	604
epiblast (generic)	8.71e-09	604
subdivision of digestive tract	3.63e-07	129
endodermal part of digestive tract	3.63e-07	129
intestine	6.40e-07	27

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	0.0189399586152364
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324004271140078
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460515749058075
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000734931221380921
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00612205560406818
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.03899839629068
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00613684476824079
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328251230338489
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139747538310034

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.