Coexpression cluster:C1048

Full id: C1048_signet_small_colon_duodenum_temporal_trachea_gall

Phase1 CAGE Peaks

Hg19::chr17:34328588..34328597,-	p2@CCL15
Hg19::chr2:201242699..201242710,+	p23@SPATS2L
Hg19::chr2:201242715..201242739,+	p12@SPATS2L
Hg19::chr2:27669034..27669075,-	p3@IFT172
Hg19::chr4:165675319..165675335,+	p1@LOC100505989
Hg19::chr4:165675340..165675345,+	p5@LOC100505989
Hg19::chr4:165675379..165675390,+	p4@LOC100505989
Hg19::chr4:165675511..165675518,+	p6@LOC100505989

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:0008201	heparin binding	0.0273314247674389
GO:0008009	chemokine activity	0.0273314247674389
GO:0042379	chemokine receptor binding	0.0273314247674389
GO:0001664	G-protein-coupled receptor binding	0.0273314247674389
GO:0005539	glycosaminoglycan binding	0.0273314247674389
GO:0006874	cellular calcium ion homeostasis	0.0273314247674389
GO:0030247	polysaccharide binding	0.0273314247674389
GO:0055074	calcium ion homeostasis	0.0273314247674389
GO:0006875	cellular metal ion homeostasis	0.0273314247674389
GO:0055065	metal ion homeostasis	0.0273314247674389
GO:0001871	pattern binding	0.0273314247674389
GO:0042330	taxis	0.0273314247674389
GO:0006935	chemotaxis	0.0273314247674389
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0278028021233909
GO:0007626	locomotory behavior	0.0278028021233909
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.0278028021233909
GO:0030003	cellular cation homeostasis	0.0278028021233909
GO:0055080	cation homeostasis	0.0278028021233909
GO:0055082	cellular chemical homeostasis	0.0291988233652572
GO:0006873	cellular ion homeostasis	0.0291988233652572
GO:0050801	ion homeostasis	0.0313145728501302
GO:0007610	behavior	0.031792812417562
GO:0048878	chemical homeostasis	0.031792812417562
GO:0005125	cytokine activity	0.031792812417562
GO:0019725	cellular homeostasis	0.036885202050857
GO:0030246	carbohydrate binding	0.0436478611125488
GO:0042592	homeostatic process	0.0436478611125488
GO:0005615	extracellular space	0.046264968808301
GO:0042221	response to chemical stimulus	0.0497852317519475

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><br>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
gastrointestinal system	1.21e-21	25
intestine	1.14e-20	17
small intestine	7.57e-20	4
subdivision of digestive tract	1.02e-17	118
digestive system	3.12e-15	145
digestive tract	3.12e-15	145
primitive gut	3.12e-15	145
endoderm-derived structure	2.20e-13	160
endoderm	2.20e-13	160
presumptive endoderm	2.20e-13	160
open tracheal system trachea	2.55e-13	2
throat	8.53e-13	2
biliary system	9.37e-11	9
biliary tree	9.37e-11	9
biliary bud	9.37e-11	9
bile duct	2.38e-09	6
digestive system duct	2.38e-09	6
duodenum	6.86e-09	2
organ system subdivision	3.60e-08	223
vermiform appendix	2.23e-07	1
caecum	2.23e-07	1
midgut	2.23e-07	1
adult organism	2.30e-07	114
submandibular gland	2.84e-07	1
submandibular gland primordium	2.84e-07	1
lower lobe of right lung	3.02e-07	1
right lung lobe	3.02e-07	1
lower lobe of lung	3.02e-07	1
lobe of lung	3.02e-07	1
right lung	3.02e-07	1
hepatopancreatic ampulla	5.50e-07	1
extrahepatic bile duct	5.50e-07	1
common bile duct	5.50e-07	1
duodenal papilla	5.50e-07	1
colon	9.81e-07	9

Disease

Ontology term	p-value	n
signet ring cell adenocarcinoma	3.06e-13	2

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
FOXA1#3169	4	5.54070987469273	0.00344427292594616	0.0175223547232155
GATA3#2625	4	13.618258178603	0.000112839652281084	0.00154677260068042

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.