Coexpression cluster:C794

Full id: C794_small_signet_adenocarcinoma_colon_Hepatocyte_gall_liver

Phase1 CAGE Peaks

Hg19::chr11:123461510..123461537,+	p@chr11:123461510..123461537 +
Hg19::chr12:49741821..49741836,+	p@chr12:49741821..49741836 +
Hg19::chr20:60987744..60987756,-	p@chr20:60987744..60987756 -
Hg19::chr3:149192427..149192438,+	p2@TM4SF4
Hg19::chr7:155754002..155754015,+	p@chr7:155754002..155754015 +
Hg19::chr7:155754027..155754046,+	p@chr7:155754027..155754046 +
Hg19::chr7:15707836..15707857,+	p1@ENST00000451240 p1@uc003ste.2
Hg19::chr7:44580861..44580912,-	p1@NPC1L1
Hg19::chr7:44580918..44580934,-	p2@NPC1L1
Hg19::chr9:130877633..130877641,-	p@chr9:130877633..130877641 -

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:0030299	cholesterol absorption	0.0135790157865837
GO:0044241	lipid digestion	0.0135790157865837
GO:0050892	intestinal absorption	0.0135790157865837
GO:0008158	hedgehog receptor activity	0.0135790157865837
GO:0015918	sterol transport	0.0135790157865837
GO:0030301	cholesterol transport	0.0135790157865837
GO:0022600	digestive system process	0.0135790157865837
GO:0006695	cholesterol biosynthetic process	0.0156323542899154
GO:0016126	sterol biosynthetic process	0.01833980188362
GO:0006487	protein amino acid N-linked glycosylation	0.0249859883709692
GO:0016324	apical plasma membrane	0.0249859883709692
GO:0044459	plasma membrane part	0.0249859883709692
GO:0008203	cholesterol metabolic process	0.0249859883709692
GO:0042157	lipoprotein metabolic process	0.0249859883709692
GO:0045177	apical part of cell	0.0249859883709692
GO:0009058	biosynthetic process	0.0249859883709692
GO:0006694	steroid biosynthetic process	0.0249859883709692
GO:0016125	sterol metabolic process	0.0249859883709692
GO:0007586	digestion	0.0249859883709692
GO:0030659	cytoplasmic vesicle membrane	0.0254574086141063
GO:0044433	cytoplasmic vesicle part	0.0254574086141063
GO:0012506	vesicle membrane	0.0256606148778984
GO:0006869	lipid transport	0.0293140852477049
GO:0006486	protein amino acid glycosylation	0.0349355291417189
GO:0043413	biopolymer glycosylation	0.0349355291417189
GO:0009101	glycoprotein biosynthetic process	0.0349355291417189
GO:0009100	glycoprotein metabolic process	0.0374071710405309
GO:0005886	plasma membrane	0.0374071710405309
GO:0008202	steroid metabolic process	0.0374071710405309
GO:0008285	negative regulation of cell proliferation	0.0374071710405309

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
kidney tubule cell	4.62e-10	12
nephron tubule epithelial cell	4.62e-10	12
metabolising cell	1.24e-08	12
endopolyploid cell	1.24e-08	12
parenchymal cell	1.24e-08	12
polyploid cell	1.24e-08	12
hepatocyte	1.24e-08	12
kidney cell	1.80e-08	18
kidney epithelial cell	1.80e-08	18
epithelial cell of nephron	3.15e-08	16

Uber Anatomy

Ontology term	p-value	n
abdomen element	4.04e-17	55
abdominal segment element	4.04e-17	55
abdominal segment of trunk	2.53e-14	61
abdomen	2.53e-14	61
trunk region element	3.39e-13	107
subdivision of digestive tract	2.58e-11	129
endodermal part of digestive tract	2.58e-11	129
gastrointestinal system	7.77e-11	35
digestive tract diverticulum	1.08e-10	23
cavitated compound organ	1.31e-10	32
immaterial anatomical entity	4.28e-10	126
sac	4.55e-10	26
renal tubule	4.62e-10	12
nephron tubule	4.62e-10	12
nephron tubule epithelium	4.62e-10	12
hepatic diverticulum	8.37e-10	22
liver primordium	8.37e-10	22
kidney	9.33e-10	27
kidney mesenchyme	9.33e-10	27
kidney rudiment	9.33e-10	27
kidney field	9.33e-10	27
epithelium of foregut-midgut junction	1.41e-09	25
anatomical boundary	1.41e-09	25
hepatobiliary system	1.41e-09	25
foregut-midgut junction	1.41e-09	25
septum transversum	1.41e-09	25
immune organ	2.19e-09	26
epithelial sac	3.16e-09	25
intraembryonic coelom	3.20e-09	21
excretory tube	3.81e-09	17
mesonephric epithelium	3.81e-09	17
mesonephric tubule	3.81e-09	17
nephric duct	3.81e-09	17
kidney epithelium	3.81e-09	17
renal duct	3.81e-09	17
mesonephric duct	3.81e-09	17
pronephric duct	3.81e-09	17
renal system	8.78e-09	45
intestine	1.20e-08	27
liver	1.27e-08	19
digestive gland	1.27e-08	19
liver bud	1.27e-08	19
digestive system	1.30e-08	155
digestive tract	1.30e-08	155
primitive gut	1.30e-08	155
gut epithelium	1.43e-08	54
mesonephros	1.95e-08	18
pronephros	1.95e-08	18
nephrogenic cord	1.95e-08	18
pronephric mesoderm	1.95e-08	18
rostral part of nephrogenic cord	1.95e-08	18
presumptive pronephric mesoderm	1.95e-08	18
nephron epithelium	3.15e-08	16
nephron	3.15e-08	16
uriniferous tubule	3.15e-08	16
metanephric mesenchyme	3.15e-08	16
nephrogenic mesenchyme	3.15e-08	16
urinary system structure	3.52e-08	44
body cavity precursor	8.98e-08	63
subdivision of trunk	1.04e-07	113
mixed endoderm/mesoderm-derived structure	1.27e-07	130
intermediate mesoderm	1.31e-07	37
adult organism	1.56e-07	115
mesenchyme	2.75e-07	238
entire embryonic mesenchyme	2.75e-07	238
urogenital ridge	3.06e-07	20
compound organ	3.70e-07	69
endocrine system	5.15e-07	45
duct	5.92e-07	26
endoderm-derived structure	9.13e-07	169
endoderm	9.13e-07	169
presumptive endoderm	9.13e-07	169

Disease

Ontology term	p-value	n
adenocarcinoma	6.42e-07	25

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	3.3869708631116	0.00921626169811418	0.0348391905128618
FOSL2#2355	4	6.77208024182468	0.00191395516386085	0.0112608621124705
HNF4A#3172	5	11.5661451814768	3.16474693899284e-05	0.00063549895320414
HNF4G#3174	4	11.5013690105787	0.000259304592032236	0.00278129940302503
MAFF#23764	2	11.263071297989	0.0129031850891221	0.0464064102594036
SREBF2#6721	2	87.3886524822695	0.000232305927155228	0.00255306731833788

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.