Coexpression cluster:C235

Full id: C235_Intestinal_Prostate_liver_colon_small_kidney_pancreas

Phase1 CAGE Peaks

Hg19::chr10:1568835..1568845,+	p1@ADARB2-AS1
Hg19::chr10:82264452..82264468,+	p@chr10:82264452..82264468 +
Hg19::chr10:82264474..82264504,+	p@chr10:82264474..82264504 +
Hg19::chr12:24768892..24768895,-	p@chr12:24768892..24768895 -
Hg19::chr12:93516455..93516485,-	p@chr12:93516455..93516485 -
Hg19::chr13:42179544..42179550,-	p@chr13:42179544..42179550 -
Hg19::chr13:92756353..92756364,+	p@chr13:92756353..92756364 +
Hg19::chr13:92756378..92756395,+	p@chr13:92756378..92756395 +
Hg19::chr13:92756423..92756437,+	p@chr13:92756423..92756437 +
Hg19::chr13:95801212..95801217,-	p@chr13:95801212..95801217 -
Hg19::chr16:64527759..64527763,-	p@chr16:64527759..64527763 -
Hg19::chr17:48764987..48765013,+	p8@ABCC3
Hg19::chr17:48765019..48765037,+	p7@ABCC3
Hg19::chr17:79990087..79990104,+	p@chr17:79990087..79990104 +
Hg19::chr19:38422775..38422794,+	p6@SIPA1L3
Hg19::chr19:41698927..41698955,+	p4@CYP2S1
Hg19::chr19:49130770..49130779,+	p@chr19:49130770..49130779 +
Hg19::chr19:49130799..49130812,+	p@chr19:49130799..49130812 +
Hg19::chr19:953515..953565,+	p@chr19:953515..953565 +
Hg19::chr1:246020583..246020602,-	p@chr1:246020583..246020602 -
Hg19::chr1:6420713..6420725,-	p16@ACOT7
Hg19::chr1:6420737..6420779,-	p9@ACOT7
Hg19::chr20:17691468..17691474,-	p@chr20:17691468..17691474 -
Hg19::chr21:45670791..45670804,-	p@chr21:45670791..45670804 -
Hg19::chr21:45670812..45670824,-	p@chr21:45670812..45670824 -
Hg19::chr21:45671014..45671052,-	p@chr21:45671014..45671052 -
Hg19::chr2:108931987..108932010,-	p@chr2:108931987..108932010 -
Hg19::chr2:165550868..165550878,-	p31@COBLL1
Hg19::chr2:205409703..205409714,+	p@chr2:205409703..205409714 +
Hg19::chr2:28340361..28340371,+	p@chr2:28340361..28340371 +
Hg19::chr2:43022486..43022490,+	p@chr2:43022486..43022490 +
Hg19::chr2:43616324..43616335,-	p@chr2:43616324..43616335 -
Hg19::chr2:43616357..43616368,-	p@chr2:43616357..43616368 -
Hg19::chr3:149388664..149388677,-	p35@WWTR1
Hg19::chr3:149388682..149388700,-	p31@WWTR1
Hg19::chr3:153375946..153375968,-	p@chr3:153375946..153375968 -
Hg19::chr3:47484661..47484686,-	p4@SCAP
Hg19::chr3:99796216..99796219,-	p@chr3:99796216..99796219 -
Hg19::chr4:121930371..121930408,+	p@chr4:121930371..121930408 +
Hg19::chr4:140048091..140048100,-	p@chr4:140048091..140048100 -
Hg19::chr4:140048110..140048120,-	p@chr4:140048110..140048120 -
Hg19::chr4:69774211..69774248,+	p@chr4:69774211..69774248 +
Hg19::chr4:69775342..69775385,+	p@chr4:69775342..69775385 +
Hg19::chr4:7168121..7168126,+	p@chr4:7168121..7168126 +
Hg19::chr4:74257875..74257904,+	p@chr4:74257875..74257904 +
Hg19::chr5:90195083..90195098,+	p6@GPR98
Hg19::chr6:22919616..22919625,-	p@chr6:22919616..22919625 -
Hg19::chr6:52616408..52616458,-	p@chr6:52616408..52616458 -
Hg19::chr6:52617751..52617757,-	p@chr6:52617751..52617757 -
Hg19::chr6:52628271..52628275,-	p1@GSTA2
Hg19::chr6:84141528..84141537,-	p@chr6:84141528..84141537 -
Hg19::chr7:115608319..115608352,-	p4@TFEC
Hg19::chr7:115608357..115608372,-	p3@TFEC
Hg19::chr7:137749883..137749887,+	p@chr7:137749883..137749887 +
Hg19::chr7:142940347..142940351,+	p@chr7:142940347..142940351 +
Hg19::chr7:83779919..83779933,-	p@chr7:83779919..83779933 -
Hg19::chr8:119760950..119760956,-	p@chr8:119760950..119760956 -
Hg19::chr9:138591077..138591111,-	p@chr9:138591077..138591111 -
Hg19::chr9:138591319..138591340,-	p1@SOHLH1
Hg19::chrX:42850716..42850719,+	p@chrX:42850716..42850719 +

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:0045596	negative regulation of cell differentiation	0.00952990698222064
GO:0051093	negative regulation of developmental process	0.00952990698222064
GO:0045599	negative regulation of fat cell differentiation	0.00952990698222064
GO:0006994	sterol depletion response, SREBP target gene transcriptional activation	0.00952990698222064
GO:0045714	regulation of low-density lipoprotein receptor biosynthetic process	0.00952990698222064
GO:0045713	low-density lipoprotein receptor biosynthetic process	0.00952990698222064
GO:0032800	receptor biosynthetic process	0.00952990698222064
GO:0045716	positive regulation of low-density lipoprotein receptor biosynthetic process	0.00952990698222064
GO:0003714	transcription corepressor activity	0.0117275625775505
GO:0030967	ER-nuclear sterol response pathway	0.0117275625775505
GO:0035104	positive regulation of sterol regulatory element binding protein target gene transcription	0.0117275625775505
GO:0045939	negative regulation of steroid metabolic process	0.0117275625775505
GO:0045541	negative regulation of cholesterol biosynthetic process	0.0117275625775505
GO:0045595	regulation of cell differentiation	0.0134504222181111
GO:0032799	low-density lipoprotein receptor metabolic process	0.0134504222181111
GO:0032933	SREBP-mediated signaling pathway	0.0134504222181111
GO:0006991	response to sterol depletion	0.0134504222181111
GO:0051055	negative regulation of lipid biosynthetic process	0.0145159930101286
GO:0045598	regulation of fat cell differentiation	0.0145159930101286
GO:0045540	regulation of cholesterol biosynthetic process	0.0145159930101286
GO:0048496	maintenance of organ identity	0.0145159930101286
GO:0003713	transcription coactivator activity	0.0155094644082816
GO:0050810	regulation of steroid biosynthetic process	0.0165649715120584
GO:0016564	transcription repressor activity	0.018285306286224
GO:0045833	negative regulation of lipid metabolic process	0.018285306286224
GO:0045893	positive regulation of transcription, DNA-dependent	0.0185734867977686
GO:0050793	regulation of developmental process	0.0199957697093771
GO:0046890	regulation of lipid biosynthetic process	0.0210120263228671
GO:0016290	palmitoyl-CoA hydrolase activity	0.0210120263228671
GO:0050794	regulation of cellular process	0.0218608434207864
GO:0045941	positive regulation of transcription	0.0223965944072342
GO:0019218	regulation of steroid metabolic process	0.0223965944072342
GO:0008514	organic anion transmembrane transporter activity	0.0223965944072342
GO:0043193	positive regulation of gene-specific transcription	0.0223965944072342
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0229576873497736
GO:0043112	receptor metabolic process	0.0232644915990176
GO:0003712	transcription cofactor activity	0.0234847394853598
GO:0032583	regulation of gene-specific transcription	0.0234847394853598
GO:0016563	transcription activator activity	0.0234847394853598
GO:0050789	regulation of biological process	0.0237586302636781
GO:0048523	negative regulation of cellular process	0.0237586302636781
GO:0048519	negative regulation of biological process	0.0258764488009861
GO:0045494	photoreceptor cell maintenance	0.0265458183502484
GO:0045444	fat cell differentiation	0.0276683402458473
GO:0031325	positive regulation of cellular metabolic process	0.0281644629784744
GO:0031324	negative regulation of cellular metabolic process	0.0299487413081397
GO:0009893	positive regulation of metabolic process	0.0308239919572163
GO:0000062	acyl-CoA binding	0.0313095896085146
GO:0065007	biological regulation	0.0313095896085146
GO:0016291	acyl-CoA thioesterase activity	0.0313095896085146
GO:0006984	ER-nuclear signaling pathway	0.0313095896085146
GO:0005622	intracellular	0.0331326485388953
GO:0008134	transcription factor binding	0.0331326485388953
GO:0009892	negative regulation of metabolic process	0.0331326485388953
GO:0006695	cholesterol biosynthetic process	0.033485908266528
GO:0001649	osteoblast differentiation	0.033485908266528
GO:0005789	endoplasmic reticulum membrane	0.033485908266528
GO:0050381	unspecific monooxygenase activity	0.033485908266528
GO:0016289	CoA hydrolase activity	0.033485908266528
GO:0042175	nuclear envelope-endoplasmic reticulum network	0.0340494306404601
GO:0019216	regulation of lipid metabolic process	0.0348701607308212
GO:0044424	intracellular part	0.0368808265656214
GO:0005504	fatty acid binding	0.0373658113617306
GO:0016126	sterol biosynthetic process	0.0386543135008576
GO:0044432	endoplasmic reticulum part	0.0386543135008576
GO:0005737	cytoplasm	0.0409718545142063
GO:0004364	glutathione transferase activity	0.0497833226662805

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	4.00e-50	4
epithelial cell of large intestine	7.14e-26	2
epithelial cell of prostate	8.00e-18	3
endodermal cell	1.72e-14	58
endo-epithelial cell	1.56e-11	42
epithelial cell of alimentary canal	5.42e-11	20

Uber Anatomy

Ontology term	p-value	n
intestinal mucosa	4.00e-50	4
wall of intestine	4.00e-50	4
gastrointestinal system mucosa	4.00e-50	4
gastrointestinal system epithelium	4.00e-50	4
intestinal epithelium	4.00e-50	4
epithelium of mucosa	9.81e-26	8
simple columnar epithelium	5.13e-23	9
anatomical wall	1.44e-17	12
gut epithelium	1.70e-15	54
rectum	1.13e-13	4
intestine	4.31e-12	17
hindgut	1.72e-11	19
lower digestive tract	3.26e-11	5
mucosa	5.42e-11	20
endo-epithelium	1.66e-10	82
gastrointestinal system	1.07e-08	25
subdivision of digestive tract	1.75e-07	118
colon	8.37e-07	9

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	15	2.77035493734636	0.00022121027126438	0.00249573074652486
FOXA2#3170	8	3.2840618336887	0.00286086895684713	0.0155060611855393
HNF4A#3172	9	3.46984355444305	0.00105182062783272	0.00743342093315887
HNF4G#3174	8	3.83378967019291	0.00108703270993606	0.00760049602952478

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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