Coexpression cluster:C4279

Full id: C4279_skeletal_diaphragm_heart_tongue_left_penis_throat

Phase1 CAGE Peaks

Hg19::chr3:12838161..12838215,+	p1@CAND2
Hg19::chr6:146056648..146056679,-	p2@EPM2A
Hg19::chr6:146056691..146056735,-	p3@EPM2A

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:0017025	TATA-binding protein binding	0.00777099123786688
GO:0005844	polysome	0.0174829288234617
GO:0005977	glycogen metabolic process	0.0370821653336492
GO:0006073	glucan metabolic process	0.0370821653336492
GO:0006112	energy reserve metabolic process	0.0370821653336492
GO:0008138	protein tyrosine/serine/threonine phosphatase activity	0.0370821653336492
GO:0043687	post-translational protein modification	0.0370821653336492
GO:0044264	cellular polysaccharide metabolic process	0.0370821653336492
GO:0005976	polysaccharide metabolic process	0.0370821653336492
GO:0006464	protein modification process	0.0378194588250887
GO:0043412	biopolymer modification	0.0378194588250887
GO:0015980	energy derivation by oxidation of organic compounds	0.0378194588250887

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
adult organism	9.38e-43	115
regional part of nervous system	3.35e-35	94
nervous system	3.35e-35	94
central nervous system	2.01e-33	82
neural tube	5.48e-31	57
neural rod	5.48e-31	57
future spinal cord	5.48e-31	57
neural keel	5.48e-31	57
brain	5.31e-29	69
future brain	5.31e-29	69
regional part of brain	7.28e-29	59
neurectoderm	4.24e-27	90
neural plate	2.19e-26	86
presumptive neural plate	2.19e-26	86
ectoderm	9.92e-26	173
presumptive ectoderm	9.92e-26	173
ectoderm-derived structure	6.95e-25	169
anterior neural tube	7.61e-24	42
regional part of forebrain	1.95e-23	41
forebrain	1.95e-23	41
future forebrain	1.95e-23	41
anterior region of body	8.67e-21	129
craniocervical region	8.67e-21	129
head	2.36e-20	123
telencephalon	9.94e-20	34
gray matter	1.01e-19	34
brain grey matter	1.01e-19	34
pre-chordal neural plate	1.36e-19	61
regional part of telencephalon	4.02e-19	33
cerebral hemisphere	1.25e-18	32
cerebral cortex	1.30e-14	25
pallium	1.30e-14	25
regional part of cerebral cortex	9.07e-14	22
neocortex	8.81e-13	20
organism subdivision	4.10e-10	365
organ part	5.48e-10	219
organ	1.11e-09	511
multi-tissue structure	2.57e-08	347
posterior neural tube	2.94e-08	15
chordal neural plate	2.94e-08	15
anatomical conduit	7.05e-08	241
anatomical cluster	1.47e-07	286
multi-cellular organism	1.47e-07	659
embryo	2.61e-07	612
tube	2.71e-07	194
segmental subdivision of nervous system	3.85e-07	13

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
BCLAF1#9774	2	14.4350984067479	0.00620114743554613	0.0273925321245613
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190577783290121
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00438026304750861
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.032335528432879
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463720572405994
GTF2B#2959	3	31.9438299343242	3.06634405746243e-05	0.000628796204628547
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108943129592905
JUNB#3726	2	20.4070884398808	0.00313146219943874	0.0164518728631814
SETDB1#9869	2	26.880017452007	0.00181446890796441	0.010896516490075
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.0390287871630684
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330366916901414

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.