Coexpression cluster:C2843

Full id: C2843_CD4_cholangiocellular_seminal_ductus_Mesenchymal_caudate_Fibroblast

Phase1 CAGE Peaks

Hg19::chr6:136172724..136172738,+	p6@PDE7B
Hg19::chr6:136172786..136172816,+	p4@PDE7B
Hg19::chr6:136172820..136172846,+	p2@PDE7B
Hg19::chr6:136173008..136173013,+	p1@PDE7B

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
muscle cell	6.06e-09	54
muscle precursor cell	8.09e-09	57
myoblast	8.09e-09	57
multi-potent skeletal muscle stem cell	8.09e-09	57
classical monocyte	2.23e-07	45
CD14-positive, CD16-negative classical monocyte	3.54e-07	42
non-terminally differentiated cell	4.44e-07	180
contractile cell	4.60e-07	59

Uber Anatomy

Ontology term	p-value	n
adult organism	2.88e-17	115
musculoskeletal system	3.98e-14	167
regional part of brain	9.30e-14	59
neural tube	9.71e-13	57
neural rod	9.71e-13	57
future spinal cord	9.71e-13	57
neural keel	9.71e-13	57
neural plate	4.79e-12	86
presumptive neural plate	4.79e-12	86
neurectoderm	5.64e-12	90
regional part of forebrain	5.73e-12	41
forebrain	5.73e-12	41
future forebrain	5.73e-12	41
anterior neural tube	7.03e-12	42
somite	8.32e-12	83
paraxial mesoderm	8.32e-12	83
presomitic mesoderm	8.32e-12	83
presumptive segmental plate	8.32e-12	83
trunk paraxial mesoderm	8.32e-12	83
presumptive paraxial mesoderm	8.32e-12	83
brain	1.02e-11	69
future brain	1.02e-11	69
pre-chordal neural plate	1.72e-11	61
anterior region of body	2.37e-11	129
craniocervical region	2.37e-11	129
gray matter	8.41e-11	34
brain grey matter	8.41e-11	34
cerebral hemisphere	1.15e-10	32
telencephalon	1.52e-10	34
head	2.20e-10	123
dermomyotome	3.07e-10	70
muscle tissue	3.52e-10	63
musculature	3.52e-10	63
musculature of body	3.52e-10	63
regional part of telencephalon	4.60e-10	33
central nervous system	6.00e-10	82
skeletal muscle tissue	1.17e-09	61
striated muscle tissue	1.17e-09	61
myotome	1.17e-09	61
regional part of cerebral cortex	7.25e-09	22
neocortex	1.26e-08	20
multi-tissue structure	7.53e-08	347
regional part of nervous system	1.28e-07	94
nervous system	1.28e-07	94
cerebral cortex	3.13e-07	25
pallium	3.13e-07	25
anatomical cluster	7.10e-07	286

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
BRCA1#672	4	20.1842306432238	6.02116732184487e-06	0.000179772639773058
CEBPB#1051	4	7.97114762582482	0.000247638578809083	0.00268568281747059
EP300#2033	4	6.7739417262232	0.000474845982144264	0.0043513590882833
JUND#3727	4	6.99466394187103	0.00041768421781858	0.00392430029010028
MAX#4149	4	6.45255550900712	0.000576761319564549	0.00486326299483303
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00889610498877768
RAD21#5885	4	10.3550338954563	8.6948481184721e-05	0.00129837180818574
REST#5978	4	9.65002871612802	0.000115282561421917	0.0015746789736259
RFX5#5993	4	12.0479108271951	4.74457429336527e-05	0.000828349372492102
SMC3#9126	4	15.0449328449328	1.95092670935632e-05	0.000439501368849147
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0323219281102328
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244951024089214
TFAP2A#7020	4	16.518634373045	1.34240829060362e-05	0.000327263724235181
TFAP2C#7022	4	10.8092286098602	7.32289634782688e-05	0.00114816990192267
TRIM28#10155	4	18.5905250452625	8.36730015875654e-06	0.000230816814918218

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.