Coexpression cluster:C1155

Full id: C1155_Hepatocyte_Intestinal_Prostate_liver_colon_small_Retinal

Phase1 CAGE Peaks

Hg19::chr11:74870848..74870885,+	p3@SLCO2B1
Hg19::chr11:74870889..74870902,+	p5@SLCO2B1
Hg19::chr11:74870904..74870913,+	p10@SLCO2B1
Hg19::chr1:209827344..209827383,-	p@chr1:209827344..209827383 -
Hg19::chr22:50738736..50738785,-	p@chr22:50738736..50738785 -
Hg19::chr6:126221034..126221056,+	p13@NCOA7
Hg19::chr6:170190148..170190182,+	p1@C6orf208

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:0016998	cell wall catabolic process	0.0139189274041004
GO:0010382	cell wall metabolic process	0.0139189274041004
GO:0007047	cell wall organization and biogenesis	0.0139189274041004
GO:0045229	external encapsulating structure organization and biogenesis	0.0139189274041004

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	6.62e-07	254

Uber Anatomy

Ontology term	p-value	n
organ	3.32e-16	511
organ part	4.15e-13	219
subdivision of digestive tract	2.52e-11	129
endodermal part of digestive tract	2.52e-11	129
endoderm-derived structure	5.77e-11	169
endoderm	5.77e-11	169
presumptive endoderm	5.77e-11	169
neural plate	7.16e-11	86
presumptive neural plate	7.16e-11	86
adult organism	8.74e-11	115
pre-chordal neural plate	3.88e-10	61
neurectoderm	5.69e-10	90
multi-tissue structure	5.95e-10	347
digestive system	8.15e-10	155
digestive tract	8.15e-10	155
primitive gut	8.15e-10	155
neural tube	8.54e-10	57
neural rod	8.54e-10	57
future spinal cord	8.54e-10	57
neural keel	8.54e-10	57
mixed endoderm/mesoderm-derived structure	1.00e-09	130
regional part of brain	3.51e-09	59
central nervous system	6.32e-09	82
anterior neural tube	1.15e-08	42
regional part of nervous system	1.21e-08	94
nervous system	1.21e-08	94
regional part of forebrain	1.36e-08	41
forebrain	1.36e-08	41
future forebrain	1.36e-08	41
brain	2.33e-08	69
future brain	2.33e-08	69
cerebral hemisphere	5.16e-08	32
head	7.11e-08	123
gray matter	7.61e-08	34
brain grey matter	7.61e-08	34
sac	8.13e-08	26
telencephalon	8.23e-08	34
digestive tract diverticulum	8.71e-08	23
multi-cellular organism	1.22e-07	659
regional part of telencephalon	1.56e-07	33
abdomen element	1.62e-07	55
abdominal segment element	1.62e-07	55
epithelium of foregut-midgut junction	1.75e-07	25
anatomical boundary	1.75e-07	25
hepatobiliary system	1.75e-07	25
foregut-midgut junction	1.75e-07	25
septum transversum	1.75e-07	25
anterior region of body	1.81e-07	129
craniocervical region	1.81e-07	129
epithelial sac	2.73e-07	25
hepatic diverticulum	3.03e-07	22
liver primordium	3.03e-07	22
embryo	5.21e-07	612
foregut	6.04e-07	98
anatomical system	6.89e-07	625
neocortex	8.00e-07	20

Disease

Ontology term	p-value	n
carcinoma	5.10e-08	106

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
EP300#2033	5	4.83852980444514	0.00113270819078547	0.00775628840397612
FOXA2#3170	4	14.0745507158087	8.60810644096383e-05	0.00128966006109284
HDAC2#3066	3	5.74955152998268	0.0115304170404053	0.0421721318607211
HEY1#23462	5	2.88579360221836	0.0123136694185303	0.0446258352558083
HNF4A#3172	5	16.5230645449669	2.94289296346546e-06	0.000100870626259064
HNF4G#3174	5	20.538158947462	1.00601446599988e-06	4.25028902971529e-05
TCF7L2#6934	4	6.15438660750705	0.00206467614813804	0.0119702849025973

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.