Coexpression cluster:C579

Full id: C579_small_argyrophil_colon_duodenum_signet_temporal_Intestinal

Phase1 CAGE Peaks

Hg19::chr10:129691195..129691212,-	p1@CLRN3
Hg19::chr11:17565907..17565933,-	p1@USH1C
Hg19::chr11:17565934..17565939,-	p8@USH1C
Hg19::chr11:17565951..17565982,-	p2@USH1C
Hg19::chr12:14849553..14849558,-	p5@GUCY2C
Hg19::chr12:14849578..14849586,-	p3@GUCY2C
Hg19::chr14:39703084..39703110,+	p10@CTAGE5
Hg19::chr16:21244993..21245042,+	p1@ANKS4B
Hg19::chr17:55163280..55163297,+	p14@AKAP1
Hg19::chr22:38506619..38506678,-	p2@BAIAP2L2
Hg19::chr2:219283836..219283853,+	p1@VIL1
Hg19::chr2:219290413..219290430,+	p@chr2:219290413..219290430 +
Hg19::chr4:40477740..40477760,-	p19@RBM47
Hg19::chr4:40477770..40477783,-	p23@RBM47
Hg19::chr7:50633078..50633140,-	p1@DDC

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:0051017	actin filament bundle formation	0.00284618870874619
GO:0007015	actin filament organization	0.00680066143724809
GO:0004058	aromatic-L-amino-acid decarboxylase activity	0.0157482632756387
GO:0030046	parallel actin filament bundle formation	0.0157482632756387
GO:0001917	photoreceptor inner segment	0.0251938834677571
GO:0051014	actin filament severing	0.0364213865634692
GO:0007168	receptor guanylyl cyclase signaling pathway	0.0364213865634692
GO:0032420	stereocilium	0.0364213865634692
GO:0032421	stereocilium bundle	0.0364213865634692
GO:0001750	photoreceptor outer segment	0.0364213865634692
GO:0030036	actin cytoskeleton organization and biogenesis	0.0364213865634692
GO:0050957	equilibrioception	0.0364213865634692
GO:0030029	actin filament-based process	0.0364213865634692
GO:0031513	nonmotile primary cilium	0.0364213865634692
GO:0004383	guanylate cyclase activity	0.0364213865634692
GO:0016829	lyase activity	0.0364213865634692
GO:0042423	catecholamine biosynthetic process	0.0364213865634692
GO:0046068	cGMP metabolic process	0.0364213865634692
GO:0006182	cGMP biosynthetic process	0.0364213865634692
GO:0042491	auditory receptor cell differentiation	0.0369540344387369
GO:0042995	cell projection	0.0369540344387369
GO:0042490	mechanoreceptor differentiation	0.0392977188640581
GO:0060113	inner ear receptor cell differentiation	0.0392977188640581
GO:0045494	photoreceptor cell maintenance	0.0392977188640581
GO:0000086	G2/M transition of mitotic cell cycle	0.0401284692083886
GO:0050885	neuromuscular process controlling balance	0.0401284692083886
GO:0005902	microvillus	0.0401284692083886
GO:0008290	F-actin capping protein complex	0.0401284692083886
GO:0051693	actin filament capping	0.0401284692083886
GO:0051016	barbed-end actin filament capping	0.0401284692083886
GO:0030835	negative regulation of actin filament depolymerization	0.0401284692083886
GO:0050905	neuromuscular process	0.0401284692083886
GO:0005903	brush border	0.0401284692083886
GO:0030834	regulation of actin filament depolymerization	0.0401284692083886
GO:0030042	actin filament depolymerization	0.0401284692083886
GO:0046847	filopodium formation	0.0401284692083886
GO:0030035	microspike biogenesis	0.0407360836108583
GO:0006584	catecholamine metabolic process	0.0423741530874236
GO:0018958	phenol metabolic process	0.0423741530874236
GO:0042472	inner ear morphogenesis	0.0423741530874236
GO:0042471	ear morphogenesis	0.0474400479121247
GO:0009975	cyclase activity	0.0481390800315232
GO:0016849	phosphorus-oxygen lyase activity	0.0481390800315232
GO:0042401	biogenic amine biosynthetic process	0.0484642007416722

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
metabolising cell	1.81e-10	12
endopolyploid cell	1.81e-10	12
parenchymal cell	1.81e-10	12
polyploid cell	1.81e-10	12
hepatocyte	1.81e-10	12
endodermal cell	1.94e-08	58
epithelial cell of stomach	1.86e-07	3

Uber Anatomy

Ontology term	p-value	n
gastrointestinal system	7.79e-36	25
intestine	4.97e-33	17
large intestine	4.64e-22	11
subdivision of digestive tract	3.57e-19	118
lower digestive tract	2.18e-16	5
digestive system	3.74e-16	145
digestive tract	3.74e-16	145
primitive gut	3.74e-16	145
colon	3.11e-14	9
endoderm-derived structure	3.92e-14	160
endoderm	3.92e-14	160
presumptive endoderm	3.92e-14	160
digestive tract diverticulum	1.09e-12	23
rectum	4.49e-12	4
epithelium of foregut-midgut junction	1.22e-11	25
anatomical boundary	1.22e-11	25
hepatobiliary system	1.22e-11	25
foregut-midgut junction	1.22e-11	25
septum transversum	1.22e-11	25
sac	4.39e-11	26
small intestine	2.45e-10	4
hepatic diverticulum	2.78e-10	22
liver primordium	2.78e-10	22
gut epithelium	3.17e-09	54
abdomen element	3.70e-09	54
abdominal segment element	3.70e-09	54
liver	4.82e-09	19
digestive gland	4.82e-09	19
liver bud	4.82e-09	19
epithelial sac	6.12e-09	25
organ system subdivision	1.84e-08	223
abdominal segment of trunk	4.89e-08	60
abdomen	4.89e-08	60
multi-tissue structure	6.61e-07	342
trunk region element	9.69e-07	101

Disease

Ontology term	p-value	n
signet ring cell adenocarcinoma	6.13e-11	2
gastrointestinal system cancer	1.03e-08	14
adenocarcinoma	9.83e-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
HDAC2#3066	5	4.47187341220875	0.00365865752308656	0.0184762116461311
HNF4A#3172	6	9.25291614518148	2.32447243124585e-05	0.000507241070302727
HNF4G#3174	4	7.66757934038581	0.00146585519209508	0.00938987060888236

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.