Coexpression cluster:C3178

Full id: C3178_Hepatocyte_mature_left_Adipocyte_pharyngeal_liver_heart

Phase1 CAGE Peaks

Hg19::chr11:63381712..63381727,-	p6@PLA2G16
Hg19::chr11:63381737..63381757,-	p4@PLA2G16
Hg19::chr11:63381763..63381783,-	p5@PLA2G16

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
fat cell	4.77e-07	15

Uber Anatomy

Ontology term	p-value	n
adult organism	8.35e-18	115
compound organ	3.56e-11	69
anatomical cluster	3.67e-11	286
body cavity precursor	1.39e-10	63
immaterial anatomical entity	6.68e-10	126
organ part	1.37e-09	219
abdominal segment of trunk	1.42e-09	61
abdomen	1.42e-09	61
anatomical cavity	1.73e-09	70
trunk region element	4.54e-09	107
anatomical conduit	1.25e-08	241
subdivision of trunk	1.50e-08	113
anatomical space	1.59e-08	104
abdomen element	4.98e-08	55
abdominal segment element	4.98e-08	55
tube	6.96e-08	194
subdivision of digestive tract	1.46e-07	129
endodermal part of digestive tract	1.46e-07	129
intermediate mesoderm	1.84e-07	37
primordium	1.90e-07	168
cavitated compound organ	3.31e-07	32
mixed endoderm/mesoderm-derived structure	4.14e-07	130
duct	4.16e-07	26
multi-tissue structure	5.15e-07	347
foregut	9.16e-07	98
urogenital ridge	9.96e-07	20

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	0.018924242980927
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323790571499884
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320597242900792
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319212248029208
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460249373837456
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00386952764407221
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108361802720645
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156209149945329
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00154489653902355
TAL1#6886	3	29.8686166774402	3.75103522793067e-05	0.00071894727137062
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00613138372729018
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328092424711813
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139665840663276

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.