Coexpression cluster:C228

Full id: C228_colon_Intestinal_Prostate_hepatoblastoma_hepatocellular_testis_adult

Phase1 CAGE Peaks

Hg19::chr10:104629450..104629461,+	p3@AS3MT
Hg19::chr10:104629528..104629542,+	p6@AS3MT
Hg19::chr10:24726425..24726450,+	p@chr10:24726425..24726450 +
Hg19::chr10:24726466..24726472,+	p@chr10:24726466..24726472 +
Hg19::chr10:71850931..71850940,+	p@chr10:71850931..71850940 +
Hg19::chr11:118082912..118082938,-	p@chr11:118082912..118082938 -
Hg19::chr11:13994430..13994436,+	p@chr11:13994430..13994436 +
Hg19::chr11:9878820..9878833,-	p@chr11:9878820..9878833 -
Hg19::chr12:102437910..102437918,-	p@chr12:102437910..102437918 -
Hg19::chr12:69726073..69726089,-	p@chr12:69726073..69726089 -
Hg19::chr12:93399748..93399757,+	p@chr12:93399748..93399757 +
Hg19::chr12:93399816..93399825,+	p@chr12:93399816..93399825 +
Hg19::chr12:93399852..93399859,+	p@chr12:93399852..93399859 +
Hg19::chr12:93399866..93399909,+	p@chr12:93399866..93399909 +
Hg19::chr12:93399913..93399929,+	p@chr12:93399913..93399929 +
Hg19::chr13:32790605..32790619,+	p@chr13:32790605..32790619 +
Hg19::chr13:32790683..32790693,+	p@chr13:32790683..32790693 +
Hg19::chr13:42179573..42179585,-	p@chr13:42179573..42179585 -
Hg19::chr13:46093155..46093164,+	p@chr13:46093155..46093164 +
Hg19::chr13:46093198..46093203,+	p@chr13:46093198..46093203 +
Hg19::chr14:22850283..22850310,-	p@chr14:22850283..22850310 -
Hg19::chr15:60749901..60749904,-	p@chr15:60749901..60749904 -
Hg19::chr15:71003168..71003184,-	p@chr15:71003168..71003184 -
Hg19::chr15:89540938..89540967,-	p@chr15:89540938..89540967 -
Hg19::chr16:19661585..19661596,+	p@chr16:19661585..19661596 +
Hg19::chr16:19661615..19661621,+	p@chr16:19661615..19661621 +
Hg19::chr16:78274724..78274726,+	p@chr16:78274724..78274726 +
Hg19::chr18:24722967..24722980,-	p4@CHST9
Hg19::chr18:24722995..24723030,-	p3@CHST9
Hg19::chr18:6929797..6929812,-	p1@uc002kng.1
Hg19::chr18:7034928..7034943,-	p@chr18:7034928..7034943 -
Hg19::chr18:7133714..7133725,-	p@chr18:7133714..7133725 -
Hg19::chr19:56653064..56653103,+	p1@AK124209
Hg19::chr1:111023361..111023366,+	p1@CYMP
Hg19::chr1:19522637..19522659,-	p@chr1:19522637..19522659 -
Hg19::chr1:19522690..19522704,-	p@chr1:19522690..19522704 -
Hg19::chr21:42694732..42694744,+	p3@FAM3B
Hg19::chr21:42694788..42694804,+	p@chr21:42694788..42694804 +
Hg19::chr2:127873614..127873626,+	p@chr2:127873614..127873626 +
Hg19::chr2:137966134..137966139,+	p@chr2:137966134..137966139 +
Hg19::chr2:176484786..176484791,+	p@chr2:176484786..176484791 +
Hg19::chr2:28340333..28340358,+	p@chr2:28340333..28340358 +
Hg19::chr2:62189730..62189756,+	p@chr2:62189730..62189756 +
Hg19::chr3:139373728..139373733,+	p@chr3:139373728..139373733 +
Hg19::chr4:107237136..107237147,+	p10@AIMP1
Hg19::chr5:142213315..142213336,+	p@chr5:142213315..142213336 +
Hg19::chr6:26500524..26500540,+	p@chr6:26500524..26500540 +
Hg19::chr6:41492615..41492636,-	p@chr6:41492615..41492636 -
Hg19::chr6:80382928..80382946,+	p@chr6:80382928..80382946 +
Hg19::chr6:8446968..8446983,+	p@chr6:8446968..8446983 +
Hg19::chr7:117329764..117329777,+	p1@ENST00000429014
Hg19::chr7:97958802..97958804,-	p@chr7:97958802..97958804 -
Hg19::chr8:55331615..55331618,+	p@chr8:55331615..55331618 +
Hg19::chr8:99425711..99425716,-	p1@ENST00000518956
Hg19::chr9:129830560..129830568,+	p@chr9:129830560..129830568 +
Hg19::chr9:138591341..138591346,-	p3@SOHLH1
Hg19::chr9:35801527..35801540,+	p@chr9:35801527..35801540 +
Hg19::chr9:71347655..71347671,+	p@chr9:71347655..71347671 +
Hg19::chrX:21849506..21849512,-	p@chrX:21849506..21849512 -
Hg19::chrX:24690735..24690744,-	p10@PCYT1B
Hg19::chrX:32583949..32583951,-	p@chrX:32583949..32583951 -
Hg19::chrX:75367265..75367270,-	p@chrX:75367265..75367270 -

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:0004105	choline-phosphate cytidylyltransferase activity	0.020116143791594
GO:0001537	N-acetylgalactosamine 4-O-sulfotransferase activity	0.020116143791594
GO:0006656	phosphatidylcholine biosynthetic process	0.020116143791594
GO:0046470	phosphatidylcholine metabolic process	0.020116143791594
GO:0043231	intracellular membrane-bound organelle	0.020116143791594
GO:0043227	membrane-bound organelle	0.020116143791594
GO:0030073	insulin secretion	0.0271777219978296
GO:0030072	peptide hormone secretion	0.0271777219978296
GO:0002790	peptide secretion	0.0271777219978296
GO:0030166	proteoglycan biosynthetic process	0.0271777219978296
GO:0043229	intracellular organelle	0.0271777219978296
GO:0043226	organelle	0.0271777219978296
GO:0005794	Golgi apparatus	0.0310458162510283
GO:0006029	proteoglycan metabolic process	0.0310458162510283
GO:0046879	hormone secretion	0.0339619745399327
GO:0015833	peptide transport	0.0353773819092401
GO:0042446	hormone biosynthetic process	0.0353773819092401
GO:0005783	endoplasmic reticulum	0.0353773819092401
GO:0046474	glycerophospholipid biosynthetic process	0.0353773819092401
GO:0030203	glycosaminoglycan metabolic process	0.0353773819092401
GO:0006022	aminoglycan metabolic process	0.0353773819092401
GO:0008146	sulfotransferase activity	0.0353773819092401
GO:0044424	intracellular part	0.0357889772004106
GO:0016782	transferase activity, transferring sulfur-containing groups	0.0386429063395159
GO:0003001	generation of a signal involved in cell-cell signaling	0.0418642014843719
GO:0006790	sulfur metabolic process	0.0486792011353691
GO:0042445	hormone metabolic process	0.0486792011353691
GO:0008654	phospholipid biosynthetic process	0.0490627688252635

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><br>

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Cell Type

Ontology term	p-value	n
intestinal epithelial cell	3.35e-66	4
epithelial cell of large intestine	3.61e-34	2
epithelial cell of prostate	3.27e-23	3
endo-epithelial cell	3.52e-15	42
epithelial cell of alimentary canal	2.58e-14	20
endodermal cell	2.67e-11	58

Uber Anatomy

Ontology term	p-value	n
intestinal mucosa	3.35e-66	4
wall of intestine	3.35e-66	4
gastrointestinal system mucosa	3.35e-66	4
gastrointestinal system epithelium	3.35e-66	4
intestinal epithelium	3.35e-66	4
epithelium of mucosa	7.68e-34	8
simple columnar epithelium	3.09e-30	9
anatomical wall	5.14e-23	12
rectum	7.35e-18	4
intestine	9.05e-16	17
hindgut	4.91e-15	19
lower digestive tract	1.40e-14	5
mucosa	2.58e-14	20
gut epithelium	4.68e-12	54
gastrointestinal system	2.77e-11	25
colon	1.04e-08	9
endo-epithelium	2.70e-08	82
large intestine	2.32e-07	11
prostate gland	2.47e-07	11
male accessory sex gland	2.47e-07	11
embryonic cloacal epithelium	2.47e-07	11
epithelium of hindgut	2.47e-07	11
urogenital sinus epithelium	2.47e-07	11
prostate bud	2.47e-07	11
prostate field	2.47e-07	11
sex gland	7.92e-07	12
male reproductive gland	7.92e-07	12

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
BHLHE40#8553	7	5.06617249723939	0.000457551318155481	0.00421729786575239
EP300#2033	20	2.18514249233006	0.00040750704601312	0.00388565948859347
FOXA1#3169	19	3.39591895545683	1.31164976046539e-06	5.20271133054482e-05
FOXA2#3170	18	7.15077979916088	2.92438537022645e-11	3.40870405894063e-09
HDAC2#3066	14	3.02933360181883	0.000153593924919596	0.00195791479612812
HNF4A#3172	13	4.85031894707094	2.06524670596649e-06	7.53641861371189e-05
HNF4G#3174	10	4.63764879458819	5.28001062848442e-05	0.000896357330995261
MAFF#23764	5	4.54156100725364	0.0049283748035772	0.0230328248136573
TCF7L2#6934	18	3.12682545381407	8.66135227406049e-06	0.00023501765917137

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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