Coexpression cluster:C133

Full id: C133_signet_gall_small_kidney_colon_ductal_adenocarcinoma

Phase1 CAGE Peaks

Hg19::chr10:105812536..105812558,+	p@chr10:105812536..105812558 +
Hg19::chr10:6777736..6777754,-	p@chr10:6777736..6777754 -
Hg19::chr10:6779446..6779460,+	p2@ENST00000417112
Hg19::chr10:98336837..98336873,-	p24@TM9SF3
Hg19::chr10:98370687..98370694,-	p@chr10:98370687..98370694 -
Hg19::chr11:67124405..67124419,-	p13@POLD4
Hg19::chr12:15885722..15885733,-	p@chr12:15885722..15885733 -
Hg19::chr12:18400438..18400444,-	p@chr12:18400438..18400444 -
Hg19::chr12:18415665..18415682,+	p@chr12:18415665..18415682 +
Hg19::chr12:18951148..18951185,+	p@chr12:18951148..18951185 +
Hg19::chr12:71559332..71559334,-	p@chr12:71559332..71559334 -
Hg19::chr12:93412598..93412606,-	p@chr12:93412598..93412606 -
Hg19::chr13:74185074..74185088,+	p@chr13:74185074..74185088 +
Hg19::chr13:74185102..74185107,+	p@chr13:74185102..74185107 +
Hg19::chr13:74185269..74185294,+	p@chr13:74185269..74185294 +
Hg19::chr13:74185299..74185308,+	p@chr13:74185299..74185308 +
Hg19::chr13:74185317..74185327,+	p@chr13:74185317..74185327 +
Hg19::chr14:101373702..101373710,-	p@chr14:101373702..101373710 -
Hg19::chr14:101373754..101373767,-	p@chr14:101373754..101373767 -
Hg19::chr14:54581722..54581743,-	p@chr14:54581722..54581743 -
Hg19::chr14:63785645..63785649,-	p1@GPHB5
Hg19::chr15:60662919..60662931,-	p@chr15:60662919..60662931 -
Hg19::chr15:60662957..60662966,-	p@chr15:60662957..60662966 -
Hg19::chr16:2031433..2031447,-	p2@NOXO1
Hg19::chr16:2031464..2031475,-	p1@NOXO1
Hg19::chr16:2141414..2141444,+	p@chr16:2141414..2141444 +
Hg19::chr16:2141513..2141528,+	p@chr16:2141513..2141528 +
Hg19::chr16:85016361..85016372,+	p@chr16:85016361..85016372 +
Hg19::chr17:39928474..39928485,-	p17@JUP
Hg19::chr17:39928501..39928513,-	p10@JUP
Hg19::chr17:39928947..39928958,-	p19@JUP
Hg19::chr17:50828983..50828988,+	p@chr17:50828983..50828988 +
Hg19::chr17:51139124..51139129,+	p@chr17:51139124..51139129 +
Hg19::chr17:56492808..56492818,-	p3@AB527734
Hg19::chr17:56492824..56492866,-	p1@AB527734
Hg19::chr17:56492878..56492893,-	p2@AB527734
Hg19::chr17:56492937..56492946,-	p11@RNF43
Hg19::chr17:56492953..56492966,-	p9@RNF43
Hg19::chr17:56492989..56493006,-	p8@RNF43
Hg19::chr17:56493024..56493038,-	p14@RNF43
Hg19::chr17:56493069..56493077,-	p10@RNF43
Hg19::chr17:67171837..67171845,-	p3@ABCA10
Hg19::chr17:67171909..67171949,-	p6@ABCA10
Hg19::chr17:67171957..67171968,-	p9@ABCA10
Hg19::chr17:73089589..73089617,+	p5@SLC16A5
Hg19::chr17:73091198..73091208,-	p@chr17:73091198..73091208 -
Hg19::chr17:73642372..73642390,+	p4@C17orf110
Hg19::chr17:73642401..73642431,+	p1@C17orf110
Hg19::chr17:73642486..73642498,+	p5@C17orf110
Hg19::chr17:73843311..73843323,-	p10@WBP2
Hg19::chr17:73843328..73843339,-	p11@WBP2
Hg19::chr17:74459187..74459193,-	p@chr17:74459187..74459193 -
Hg19::chr17:74459285..74459291,-	p@chr17:74459285..74459291 -
Hg19::chr17:74459307..74459308,-	p@chr17:74459307..74459308 -
Hg19::chr17:74459348..74459359,-	p@chr17:74459348..74459359 -
Hg19::chr18:12701539..12701579,+	p@chr18:12701539..12701579 +
Hg19::chr18:12701647..12701671,+	p@chr18:12701647..12701671 +
Hg19::chr19:1654223..1654233,-	p@chr19:1654223..1654233 -
Hg19::chr19:1654251..1654268,-	p@chr19:1654251..1654268 -
Hg19::chr19:1753387..1753395,-	p@chr19:1753387..1753395 -
Hg19::chr1:174872019..174872028,+	p@chr1:174872019..174872028 +
Hg19::chr1:178009766..178009803,+	p@chr1:178009766..178009803 +
Hg19::chr1:183976829..183976846,-	p@chr1:183976829..183976846 -
Hg19::chr1:183976861..183976878,-	p@chr1:183976861..183976878 -
Hg19::chr1:183976888..183976895,-	p@chr1:183976888..183976895 -
Hg19::chr1:184005350..184005356,-	p@chr1:184005350..184005356 -
Hg19::chr1:187929716..187929735,+	p@chr1:187929716..187929735 +
Hg19::chr1:188011911..188011936,+	p@chr1:188011911..188011936 +
Hg19::chr1:205905031..205905037,-	p4@SLC26A9
Hg19::chr1:233843247..233843266,-	p@chr1:233843247..233843266 -
Hg19::chr1:233843288..233843295,-	p@chr1:233843288..233843295 -
Hg19::chr1:53890334..53890349,+	p@chr1:53890334..53890349 +
Hg19::chr1:53919202..53919204,-	p@chr1:53919202..53919204 -
Hg19::chr20:25176450..25176471,+	p2@ENTPD6
Hg19::chr21:25744883..25744889,-	p@chr21:25744883..25744889 -
Hg19::chr2:168920401..168920426,-	p@chr2:168920401..168920426 -
Hg19::chr2:174136708..174136746,-	p2@MLK7-AS1
Hg19::chr2:220034719..220034742,-	p1@SLC23A3
Hg19::chr2:220034745..220034768,-	p2@SLC23A3
Hg19::chr2:231965004..231965009,-	p@chr2:231965004..231965009 -
Hg19::chr2:242312343..242312376,+	p4@FARP2
Hg19::chr2:27528919..27528940,+	p@chr2:27528919..27528940 +
Hg19::chr2:27529044..27529063,+	p@chr2:27529044..27529063 +
Hg19::chr2:27529068..27529081,+	p@chr2:27529068..27529081 +
Hg19::chr2:27529092..27529098,+	p@chr2:27529092..27529098 +
Hg19::chr2:99902552..99902557,+	p@chr2:99902552..99902557 +
Hg19::chr3:14058640..14058664,+	p9@TPRXL
Hg19::chr3:14058772..14058785,+	p7@TPRXL
Hg19::chr3:14058794..14058815,+	p1@TPRXL
Hg19::chr3:14061155..14061180,+	p8@TPRXL
Hg19::chr3:142285096..142285107,-	p@chr3:142285096..142285107 -
Hg19::chr3:149193579..149193585,+	p9@TM4SF4
Hg19::chr3:168991187..168991198,-	p@chr3:168991187..168991198 -
Hg19::chr3:168991209..168991221,-	p@chr3:168991209..168991221 -
Hg19::chr3:168991629..168991647,-	p@chr3:168991629..168991647 -
Hg19::chr3:169101687..169101694,-	p@chr3:169101687..169101694 -
Hg19::chr3:169101737..169101746,-	p@chr3:169101737..169101746 -
Hg19::chr3:169101774..169101782,-	p@chr3:169101774..169101782 -
Hg19::chr3:42226097..42226118,+	p@chr3:42226097..42226118 +
Hg19::chr3:94366924..94366944,+	p@chr3:94366924..94366944 +
Hg19::chr4:22270286..22270327,-	p@chr4:22270286..22270327 -
Hg19::chr4:77637382..77637399,+	p13@SHROOM3
Hg19::chr4:77637400..77637431,+	p7@SHROOM3
Hg19::chr5:114750892..114750903,-	p@chr5:114750892..114750903 -
Hg19::chr5:114750907..114750924,-	p@chr5:114750907..114750924 -
Hg19::chr5:135880548..135880583,-	p@chr5:135880548..135880583 -
Hg19::chr5:164891824..164891866,-	p@chr5:164891824..164891866 -
Hg19::chr6:106905153..106905161,-	p@chr6:106905153..106905161 -
Hg19::chr6:24193738..24193759,-	p@chr6:24193738..24193759 -
Hg19::chr6:34208414..34208429,+	p16@HMGA1
Hg19::chr7:116451016..116451023,+	p8@CAPZA2
Hg19::chr7:117120106..117120117,+	p5@CFTR
Hg19::chr7:117355858..117355864,-	p@chr7:117355858..117355864 -
Hg19::chr7:117355869..117355891,-	p@chr7:117355869..117355891 -
Hg19::chr7:117355907..117355916,-	p@chr7:117355907..117355916 -
Hg19::chr7:117355930..117355937,-	p@chr7:117355930..117355937 -
Hg19::chr7:117355942..117355945,-	p@chr7:117355942..117355945 -
Hg19::chr7:117356954..117356963,-	p@chr7:117356954..117356963 -
Hg19::chr7:960422..960430,-	p20@ADAP1
Hg19::chr7:960534..960548,-	p16@ADAP1
Hg19::chr8:17918981..17918993,-	p14@ASAH1
Hg19::chr8:66639520..66639548,-	p@chr8:66639520..66639548 -
Hg19::chr9:139312981..139312986,+	p4@PMPCA
Hg19::chr9:139313013..139313034,+	p3@PMPCA
Hg19::chr9:14300257..14300268,-	p@chr9:14300257..14300268 -
Hg19::chr9:3898759..3898766,-	p@chr9:3898759..3898766 -
Hg19::chr9:3898804..3898817,-	p@chr9:3898804..3898817 -
Hg19::chr9:3898831..3898843,-	p@chr9:3898831..3898843 -
Hg19::chr9:3899086..3899097,-	p@chr9:3899086..3899097 -
Hg19::chr9:3900888..3900935,-	p@chr9:3900888..3900935 -
Hg19::chr9:74355313..74355333,-	p@chr9:74355313..74355333 -
Hg19::chrX:132849095..132849103,+	p@chrX:132849095..132849103 +
Hg19::chrX:69698896..69698934,+	p7@DLG3
Hg19::chrX:76923993..76924035,-	p@chrX:76923993..76924035 -
Hg19::chrX:96374877..96374886,+	p@chrX:96374877..96374886 +
Hg19::chrX:96374896..96374901,+	p@chrX:96374896..96374901 +

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:0005912	adherens junction	0.00215716088844199
GO:0001936	regulation of endothelial cell proliferation	0.00898727966365281
GO:0001935	endothelial cell proliferation	0.00898727966365281
GO:0042127	regulation of cell proliferation	0.0194174866352181
GO:0030324	lung development	0.021744029977528
GO:0030323	respiratory tube development	0.021744029977528
GO:0008285	negative regulation of cell proliferation	0.021744029977528
GO:0008092	cytoskeletal protein binding	0.0245014610963039
GO:0005515	protein binding	0.0245014610963039
GO:0005224	ATP-binding and phosphorylation-dependent chloride channel activity	0.0245014610963039
GO:0005260	channel-conductance-controlling ATPase activity	0.0245014610963039
GO:0005624	membrane fraction	0.0255493356009633
GO:0016324	apical plasma membrane	0.0255493356009633
GO:0006820	anion transport	0.0255493356009633
GO:0008283	cell proliferation	0.0255493356009633
GO:0042975	peroxisome proliferator activated receptor binding	0.0255493356009633
GO:0043482	cellular pigment accumulation	0.0255493356009633
GO:0004240	mitochondrial processing peptidase activity	0.0255493356009633
GO:0043476	pigment accumulation	0.0255493356009633
GO:0006345	loss of chromatin silencing	0.0255493356009633
GO:0003680	AT DNA binding	0.0255493356009633
GO:0045177	apical part of cell	0.0255493356009633
GO:0051128	regulation of cellular component organization and biogenesis	0.0310797031657759
GO:0016020	membrane	0.0310797031657759
GO:0016322	neuron remodeling	0.0310797031657759
GO:0033059	cellular pigmentation	0.0310797031657759
GO:0000267	cell fraction	0.0332688085403726
GO:0030054	cell junction	0.0347455676759035
GO:0035295	tube development	0.0347455676759035
GO:0003891	delta DNA polymerase activity	0.0347455676759035
GO:0046965	retinoid X receptor binding	0.0347455676759035
GO:0017110	nucleoside-diphosphatase activity	0.0384569858713336
GO:0005916	fascia adherens	0.0384569858713336
GO:0006337	nucleosome disassembly	0.0384569858713336
GO:0031498	chromatin disassembly	0.0384569858713336
GO:0001938	positive regulation of endothelial cell proliferation	0.042492581409193
GO:0015355	secondary active monocarboxylate transmembrane transporter activity	0.042492581409193
GO:0009898	internal side of plasma membrane	0.042492581409193
GO:0045815	positive regulation of gene expression, epigenetic	0.0459337426993214
GO:0031116	positive regulation of microtubule polymerization	0.0459337426993214
GO:0050998	nitric-oxide synthase binding	0.0459337426993214
GO:0048523	negative regulation of cellular process	0.04677588402999
GO:0030321	transepithelial chloride transport	0.04677588402999
GO:0031112	positive regulation of microtubule polymerization or depolymerization	0.04677588402999
GO:0031113	regulation of microtubule polymerization	0.04677588402999
GO:0045176	apical protein localization	0.04677588402999
GO:0048519	negative regulation of biological process	0.0493865270640579
GO:0016601	Rac protein signal transduction	0.0493865270640579
GO:0042974	retinoic acid receptor binding	0.0493865270640579

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
epithelial cell	2.49e-21	254
endodermal cell	5.09e-12	59
endo-epithelial cell	2.37e-09	43

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	2.19e-23	169
endoderm	2.19e-23	169
presumptive endoderm	2.19e-23	169
multi-tissue structure	1.72e-22	347
digestive system	6.29e-22	155
digestive tract	6.29e-22	155
primitive gut	6.29e-22	155
subdivision of digestive tract	1.11e-21	129
endodermal part of digestive tract	1.11e-21	129
mixed endoderm/mesoderm-derived structure	5.74e-18	130
trunk region element	3.23e-16	107
organ	3.52e-16	511
immaterial anatomical entity	3.82e-16	126
foregut	4.16e-15	98
mesenchyme	7.33e-15	238
entire embryonic mesenchyme	7.33e-15	238
embryo	1.21e-14	612
anatomical conduit	5.69e-14	241
primordium	6.06e-14	168
germ layer	9.72e-14	604
embryonic tissue	9.72e-14	604
presumptive structure	9.72e-14	604
epiblast (generic)	9.72e-14	604
embryonic structure	1.16e-13	605
developing anatomical structure	1.16e-13	605
anatomical space	5.29e-13	104
anatomical cluster	9.90e-13	286
endo-epithelium	4.66e-12	82
organism subdivision	6.04e-12	365
epithelium	1.06e-11	309
cell layer	1.31e-11	312
anatomical system	2.25e-11	625
anatomical group	3.48e-11	626
multi-cellular organism	4.22e-11	659
subdivision of trunk	1.66e-10	113
gastrointestinal system	1.15e-09	35
tube	1.16e-09	194
respiratory system	5.09e-09	72
trunk	6.87e-09	216
organ part	1.06e-08	219
anatomical cavity	1.82e-08	70
urinary system structure	1.99e-08	44
renal system	2.20e-08	45
adult organism	3.21e-08	115
compound organ	3.38e-08	69
abdomen element	6.49e-08	55
abdominal segment element	6.49e-08	55
epithelial fold	7.93e-08	51
gut epithelium	9.88e-08	54
intestine	1.37e-07	27
organ segment	3.32e-07	97
cavitated compound organ	4.48e-07	32
epithelial bud	4.86e-07	37
body cavity precursor	7.20e-07	63
reproductive structure	8.03e-07	59
reproductive system	8.03e-07	59
gland	8.94e-07	59

Disease

Ontology term	p-value	n
carcinoma	9.45e-22	106
cell type cancer	2.44e-11	143
adenocarcinoma	2.16e-09	25
squamous cell carcinoma	1.29e-07	14

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
PRDM1#639	5	4.84672631534782	0.00396228780051937	0.0190182166275308

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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