Coexpression cluster:C190

Full id: C190_colon_small_rectum_duodenum_appendix_temporal_oral

Phase1 CAGE Peaks

Hg19::chr10:112657988..112657991,+	p35@PDCD4
Hg19::chr10:14574705..14574718,-	p18@FAM107B
Hg19::chr11:114430588..114430608,-	p1@FAM55A
Hg19::chr11:114466471..114466474,-	p4@FAM55D
Hg19::chr11:114522262..114522267,-	p@chr11:114522262..114522267 -
Hg19::chr11:118500762..118500765,+	p11@PHLDB1
Hg19::chr11:130059981..130060005,+	p5@ST14
Hg19::chr11:17036137..17036152,-	p3@PLEKHA7
Hg19::chr11:46958029..46958041,+	p4@C11orf49
Hg19::chr11:76746720..76746738,-	p@chr11:76746720..76746738 -
Hg19::chr12:27849378..27849385,+	p1@REP15
Hg19::chr14:47203595..47203635,-	p@chr14:47203595..47203635 -
Hg19::chr15:40648362..40648364,+	p@chr15:40648362..40648364 +
Hg19::chr15:41120932..41120960,-	p2@PPP1R14D
Hg19::chr15:41224934..41224945,-	p@chr15:41224934..41224945 -
Hg19::chr16:2034635..2034644,+	p12@GFER
Hg19::chr16:25228264..25228273,+	p1@AQP8
Hg19::chr16:29760335..29760341,+	p@chr16:29760335..29760341 +
Hg19::chr16:29789573..29789606,+	p1@ZG16
Hg19::chr16:67464830..67464845,-	p@chr16:67464830..67464845 -
Hg19::chr16:67465190..67465197,+	p4@HSD11B2
Hg19::chr16:67475274..67475285,-	p7@ATP6V0D1
Hg19::chr16:79632234..79632245,-	p@chr16:79632234..79632245 -
Hg19::chr16:79804394..79804433,-	p@chr16:79804394..79804433 -
Hg19::chr17:26800296..26800314,+	p4@SLC13A2
Hg19::chr17:42031300..42031313,-	p1@PYY
Hg19::chr17:74639886..74639899,-	p3@ST6GALNAC1
Hg19::chr19:3025659..3025672,-	p6@TLE2
Hg19::chr19:39297150..39297157,-	p@chr19:39297150..39297157 -
Hg19::chr19:39303110..39303129,-	p@chr19:39303110..39303129 -
Hg19::chr19:42190911..42190925,-	p@chr19:42190911..42190925 -
Hg19::chr19:42192156..42192171,-	p2@CEACAM7
Hg19::chr19:42192189..42192207,-	p1@CEACAM7
Hg19::chr19:56200410..56200417,+	p@chr19:56200410..56200417 +
Hg19::chr19:7456079..7456083,-	p@chr19:7456079..7456083 -
Hg19::chr1:149908217..149908248,-	p4@MTMR11
Hg19::chr1:167059763..167059776,-	p4@GPA33
Hg19::chr1:20141662..20141673,-	p4@RNF186
Hg19::chr1:20141681..20141690,-	p5@RNF186
Hg19::chr1:20141728..20141745,-	p3@RNF186
Hg19::chr1:207241396..207241407,+	p@chr1:207241396..207241407 +
Hg19::chr1:220100976..220100981,-	p@chr1:220100976..220100981 -
Hg19::chr1:220101892..220101906,-	p1@SLC30A10
Hg19::chr1:35150899..35150929,-	p@chr1:35150899..35150929 -
Hg19::chr1:47905805..47905807,+	p@chr1:47905805..47905807 +
Hg19::chr21:43733776..43733803,-	p3@TFF3
Hg19::chr2:128375443..128375446,+	p@chr2:128375443..128375446 +
Hg19::chr2:201242765..201242779,+	p26@SPATS2L
Hg19::chr2:241625719..241625734,+	p3@ENST00000407635
Hg19::chr2:241625749..241625758,+	p6@ENST00000407635
Hg19::chr3:124355991..124356002,+	p32@KALRN
Hg19::chr3:124646625..124646633,-	p11@MUC13
Hg19::chr3:124646645..124646669,-	p3@MUC13
Hg19::chr4:150822397..150822409,-	p@chr4:150822397..150822409 -
Hg19::chr4:165675294..165675306,+	p3@LOC100505989
Hg19::chr4:667307..667315,+	p17@MYL5
Hg19::chr4:81974774..81974778,+	p@chr4:81974774..81974778 +
Hg19::chr4:89708946..89708956,-	p@chr4:89708946..89708956 -
Hg19::chr4:89730993..89730995,-	p@chr4:89730993..89730995 -
Hg19::chr5:149340464..149340483,+	p2@SLC26A2
Hg19::chr5:149363028..149363035,+	p12@SLC26A2
Hg19::chr5:150829073..150829087,+	p10@SLC36A1
Hg19::chr5:150829095..150829107,+	p9@SLC36A1
Hg19::chr5:156496412..156496429,-	p@chr5:156496412..156496429 -
Hg19::chr5:160112366..160112378,-	p7@ATP10B
Hg19::chr5:160112386..160112405,-	p3@ATP10B
Hg19::chr5:160112418..160112436,-	p4@ATP10B
Hg19::chr5:160112447..160112454,-	p9@ATP10B
Hg19::chr6:110887812..110887830,-	p@chr6:110887812..110887830 -
Hg19::chr6:80340818..80340825,+	p7@SH3BGRL2
Hg19::chr7:100612141..100612155,-	p@chr7:100612141..100612155 -
Hg19::chr7:87856280..87856298,-	p2@SRI
Hg19::chr7:87856303..87856312,-	p3@SRI
Hg19::chr7:92848861..92848873,-	p7@HEPACAM2
Hg19::chr7:92848878..92848889,-	p2@HEPACAM2
Hg19::chr8:146253359..146253362,-	p@chr8:146253359..146253362 -
Hg19::chr8:24262894..24262908,+	p6@ADAMDEC1
Hg19::chr8:24262931..24262946,+	p5@ADAMDEC1
Hg19::chr8:24262965..24262986,+	p@chr8:24262965..24262986 +
Hg19::chr8:24262988..24262999,+	p@chr8:24262988..24262999 +
Hg19::chr8:24263041..24263045,+	p@chr8:24263041..24263045 +
Hg19::chr8:8559690..8559736,+	p2@CLDN23
Hg19::chr9:139658967..139658975,-	p1@LCN15
Hg19::chr9:139683392..139683395,-	p@chr9:139683392..139683395 -
Hg19::chr9:139688064..139688089,+	p@chr9:139688064..139688089 +
Hg19::chr9:26994531..26994535,-	p@chr9:26994531..26994535 -
Hg19::chr9:27005657..27005675,-	p1@LRRC19
Hg19::chrX:15620273..15620294,-	p3@ACE2

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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p.value	FDR	nGenes	nPathway	Name
1.89711789408108e-05	0.0120087562695332	6	401	Transmembrane transport of small molecules (Reactome):REACT_15518

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:0016021	integral to membrane	0.0208338023654932
GO:0031224	intrinsic to membrane	0.0208338023654932
GO:0044425	membrane part	0.0285712177267866
GO:0022804	active transmembrane transporter activity	0.0338759110886178
GO:0005886	plasma membrane	0.0338759110886178
GO:0006937	regulation of muscle contraction	0.0338759110886178
GO:0022857	transmembrane transporter activity	0.0338759110886178
GO:0015361	low affinity sodium:dicarboxylate symporter activity	0.0338759110886178
GO:0001665	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity	0.0338759110886178
GO:0001977	renal regulation of blood volume	0.0338759110886178
GO:0002017	aldosterone mediated regulation of blood volume	0.0338759110886178
GO:0003845	11-beta-hydroxysteroid dehydrogenase activity	0.0338759110886178
GO:0022892	substrate-specific transporter activity	0.0338759110886178
GO:0015075	ion transmembrane transporter activity	0.0338759110886178
GO:0005774	vacuolar membrane	0.0338759110886178
GO:0044437	vacuolar part	0.0338759110886178
GO:0032328	alanine transport	0.0338759110886178
GO:0001618	viral receptor activity	0.0338759110886178
GO:0015808	L-alanine transport	0.0338759110886178
GO:0015193	L-proline transmembrane transporter activity	0.0338759110886178
GO:0016972	thiol oxidase activity	0.0338759110886178
GO:0015180	L-alanine transmembrane transporter activity	0.0338759110886178
GO:0006880	intracellular sequestering of iron ion	0.0338759110886178
GO:0015816	glycine transport	0.0338759110886178
GO:0043508	negative regulation of JNK activity	0.0338759110886178
GO:0022858	alanine transmembrane transporter activity	0.0338759110886178
GO:0016020	membrane	0.0338759110886178
GO:0015824	proline transport	0.046281544289703
GO:0003071	renal regulation of systemic arterial blood pressure	0.046281544289703
GO:0022891	substrate-specific transmembrane transporter activity	0.0479725523165227

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><br>

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Uber Anatomy

Ontology term	p-value	n
intestine	6.33e-54	17
gastrointestinal system	3.24e-37	25
large intestine	4.21e-35	11
small intestine	3.34e-28	4
colon	8.11e-28	9
vermiform appendix	1.65e-16	1
caecum	1.65e-16	1
midgut	1.65e-16	1
lower digestive tract	3.23e-13	5
digestive system	1.00e-07	145
digestive tract	1.00e-07	145
primitive gut	1.00e-07	145
subdivision of digestive tract	1.20e-07	118
endoderm-derived structure	6.42e-07	160
endoderm	6.42e-07	160
presumptive endoderm	6.42e-07	160

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	20	2.51850448849669	9.2020631476479e-05	0.00134038252869902
FOXA2#3170	16	4.47826613684823	4.79909341517431e-07	2.26281046134262e-05
HNF4A#3172	11	2.89153629536921	0.00145466616250973	0.00932506011210125
HNF4G#3174	10	3.26743437800532	0.000979147246418692	0.00703599554621726

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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