Coexpression cluster:C169

Full id: C169_hereditary_adult_gall_lymphangiectasia_chronic_b_choriocarcinoma

Phase1 CAGE Peaks

Hg19::chr10:129780311..129780325,+	p@chr10:129780311..129780325 +
Hg19::chr11:12017002..12017006,-	p@chr11:12017002..12017006 -
Hg19::chr11:45077600..45077605,-	p@chr11:45077600..45077605 -
Hg19::chr12:101114061..101114068,+	p@chr12:101114061..101114068 +
Hg19::chr12:111115637..111115643,-	p@chr12:111115637..111115643 -
Hg19::chr12:129886232..129886236,+	p@chr12:129886232..129886236 +
Hg19::chr12:54430774..54430776,+	p@chr12:54430774..54430776 +
Hg19::chr12:54430838..54430849,+	p@chr12:54430838..54430849 +
Hg19::chr12:54430878..54430894,+	p@chr12:54430878..54430894 +
Hg19::chr13:36788658..36788703,-	p2@CCDC169-SOHLH2 p2@SOHLH2
Hg19::chr13:36788718..36788729,-	p3@CCDC169-SOHLH2 p3@SOHLH2
Hg19::chr13:90031692..90031701,-	p@chr13:90031692..90031701 -
Hg19::chr13:90054694..90054707,+	p@chr13:90054694..90054707 +
Hg19::chr13:98832731..98832745,+	p@chr13:98832731..98832745 +
Hg19::chr14:100485632..100485641,-	p@chr14:100485632..100485641 -
Hg19::chr14:100485707..100485728,-	p@chr14:100485707..100485728 -
Hg19::chr14:100485712..100485727,+	p14@EVL
Hg19::chr14:100485738..100485745,+	p37@EVL
Hg19::chr14:106347250..106347263,-	p@chr14:106347250..106347263 -
Hg19::chr14:106453005..106453010,-	p1@HM995871
Hg19::chr14:25495787..25495796,-	p@chr14:25495787..25495796 -
Hg19::chr14:72944734..72944763,+	p@chr14:72944734..72944763 +
Hg19::chr14:93336950..93336968,-	p@chr14:93336950..93336968 -
Hg19::chr15:23841916..23841926,-	p@chr15:23841916..23841926 -
Hg19::chr15:52404898..52404917,-	p4@BCL2L10
Hg19::chr15:52404921..52404940,-	p2@BCL2L10
Hg19::chr15:83368645..83368652,-	p@chr15:83368645..83368652 -
Hg19::chr15:96537325..96537333,-	p@chr15:96537325..96537333 -
Hg19::chr15:96539848..96539851,-	p@chr15:96539848..96539851 -
Hg19::chr15:99539699..99539703,+	p@chr15:99539699..99539703 +
Hg19::chr16:55880765..55880779,-	p@chr16:55880765..55880779 -
Hg19::chr17:11711799..11711827,-	p@chr17:11711799..11711827 -
Hg19::chr17:21251902..21251907,-	p@chr17:21251902..21251907 -
Hg19::chr17:34206860..34206865,-	p@chr17:34206860..34206865 -
Hg19::chr17:51127122..51127127,-	p@chr17:51127122..51127127 -
Hg19::chr17:51147371..51147377,+	p@chr17:51147371..51147377 +
Hg19::chr17:59322535..59322541,-	p@chr17:59322535..59322541 -
Hg19::chr17:59322564..59322600,+	p5@BCAS3
Hg19::chr17:60536002..60536040,+	p4@TLK2
Hg19::chr17:70016724..70016733,-	p@chr17:70016724..70016733 -
Hg19::chr18:56320706..56320709,+	p@chr18:56320706..56320709 +
Hg19::chr18:59518131..59518142,-	p@chr18:59518131..59518142 -
Hg19::chr18:59518164..59518170,-	p@chr18:59518164..59518170 -
Hg19::chr18:60662408..60662414,+	p@chr18:60662408..60662414 +
Hg19::chr19:28913175..28913210,+	p@chr19:28913175..28913210 +
Hg19::chr1:15482761..15482763,-	p@chr1:15482761..15482763 -
Hg19::chr1:15563005..15563040,+	p@chr1:15563005..15563040 +
Hg19::chr1:15563067..15563079,+	p@chr1:15563067..15563079 +
Hg19::chr1:159267075..159267096,+	p@chr1:159267075..159267096 +
Hg19::chr1:210573062..210573064,-	p@chr1:210573062..210573064 -
Hg19::chr1:229504069..229504072,-	p@chr1:229504069..229504072 -
Hg19::chr1:24581338..24581346,-	p1@uc001biw.2
Hg19::chr1:24581364..24581374,-	p@chr1:24581364..24581374 -
Hg19::chr1:25876348..25876361,+	p5@LDLRAP1
Hg19::chr1:25876368..25876381,+	p6@LDLRAP1
Hg19::chr1:25876405..25876417,+	p8@LDLRAP1
Hg19::chr20:25475219..25475229,-	p@chr20:25475219..25475229 -
Hg19::chr20:56058118..56058120,-	p@chr20:56058118..56058120 -
Hg19::chr20:56058449..56058484,+	p@chr20:56058449..56058484 +
Hg19::chr20:59009589..59009592,+	p@chr20:59009589..59009592 +
Hg19::chr22:25075039..25075064,+	p@chr22:25075039..25075064 +
Hg19::chr22:25075096..25075120,+	p@chr22:25075096..25075120 +
Hg19::chr22:33206569..33206577,+	p@chr22:33206569..33206577 +
Hg19::chr22:33206603..33206608,+	p@chr22:33206603..33206608 +
Hg19::chr22:33206615..33206622,+	p@chr22:33206615..33206622 +
Hg19::chr22:33221188..33221202,+	p@chr22:33221188..33221202 +
Hg19::chr22:47883693..47883699,-	p@chr22:47883693..47883699 -
Hg19::chr2:135361356..135361362,-	p@chr2:135361356..135361362 -
Hg19::chr2:173750319..173750340,-	p@chr2:173750319..173750340 -
Hg19::chr2:206489395..206489396,-	p@chr2:206489395..206489396 -
Hg19::chr2:45490454..45490486,-	p@chr2:45490454..45490486 -
Hg19::chr3:106921810..106921817,-	p@chr3:106921810..106921817 -
Hg19::chr3:106921835..106921857,-	p@chr3:106921835..106921857 -
Hg19::chr3:128579995..128580003,+	p@chr3:128579995..128580003 +
Hg19::chr3:133185639..133185654,+	p@chr3:133185639..133185654 +
Hg19::chr3:184113225..184113231,-	p@chr3:184113225..184113231 -
Hg19::chr3:25449881..25449891,-	p@chr3:25449881..25449891 -
Hg19::chr4:170719812..170719813,+	p@chr4:170719812..170719813 +
Hg19::chr5:132587921..132587932,-	p5@FSTL4
Hg19::chr5:132587961..132587985,-	p3@FSTL4
Hg19::chr6:144724237..144724255,+	p@chr6:144724237..144724255 +
Hg19::chr6:32582541..32582590,-	p@chr6:32582541..32582590 -
Hg19::chr7:140980284..140980289,+	p@chr7:140980284..140980289 +
Hg19::chr7:22136603..22136614,+	p@chr7:22136603..22136614 +
Hg19::chr7:69393144..69393149,-	p@chr7:69393144..69393149 -
Hg19::chr7:69393274..69393286,+	p@chr7:69393274..69393286 +
Hg19::chr7:70419611..70419618,+	p@chr7:70419611..70419618 +
Hg19::chr8:105291143..105291166,-	p@chr8:105291143..105291166 -
Hg19::chr8:12898422..12898427,-	p@chr8:12898422..12898427 -
Hg19::chr8:12999595..12999600,+	p@chr8:12999595..12999600 +
Hg19::chr8:13199276..13199284,+	p@chr8:13199276..13199284 +
Hg19::chr8:13199316..13199325,+	p@chr8:13199316..13199325 +
Hg19::chr8:13526697..13526704,+	p@chr8:13526697..13526704 +
Hg19::chr8:138082720..138082726,-	p@chr8:138082720..138082726 -
Hg19::chr8:22559267..22559271,-	p@chr8:22559267..22559271 -
Hg19::chr8:86174690..86174727,+	p@chr8:86174690..86174727 +
Hg19::chr9:124116019..124116044,-	p@chr9:124116019..124116044 -
Hg19::chr9:124116047..124116052,-	p@chr9:124116047..124116052 -
Hg19::chr9:124632999..124633011,-	p@chr9:124632999..124633011 -
Hg19::chr9:35194941..35194952,-	p@chr9:35194941..35194952 -
Hg19::chr9:80847589..80847596,-	p@chr9:80847589..80847596 -
Hg19::chrX:46811494..46811522,-	p@chrX:46811494..46811522 -
Hg19::chrX:71093307..71093345,-	p@chrX:71093307..71093345 -

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:0016323	basolateral plasma membrane	0.0201253396018479
GO:0001672	regulation of chromatin assembly or disassembly	0.0201253396018479
GO:0015460	transport accessory protein activity	0.0201253396018479
GO:0048260	positive regulation of receptor-mediated endocytosis	0.0201253396018479
GO:0030121	AP-1 adaptor complex	0.0201253396018479
GO:0030669	clathrin-coated endocytic vesicle membrane	0.0201253396018479
GO:0030128	clathrin coat of endocytic vesicle	0.0201253396018479
GO:0030122	AP-2 adaptor complex	0.0201253396018479
GO:0005522	profilin binding	0.0201253396018479
GO:0001784	phosphotyrosine binding	0.0201253396018479
GO:0045309	protein phosphorylated amino acid binding	0.0201253396018479
GO:0030666	endocytic vesicle membrane	0.0201253396018479
GO:0045334	clathrin-coated endocytic vesicle	0.0201253396018479
GO:0048259	regulation of receptor-mediated endocytosis	0.0201253396018479
GO:0051219	phosphoprotein binding	0.0268120729752947
GO:0030276	clathrin binding	0.0268120729752947
GO:0043393	regulation of protein binding	0.0268120729752947
GO:0030132	clathrin coat of coated pit	0.0268120729752947
GO:0042632	cholesterol homeostasis	0.0268120729752947
GO:0055092	sterol homeostasis	0.0268120729752947
GO:0045178	basal part of cell	0.0268120729752947
GO:0009925	basal plasma membrane	0.0268120729752947
GO:0030130	clathrin coat of trans-Golgi network vesicle	0.0268120729752947
GO:0055088	lipid homeostasis	0.0268120729752947
GO:0045807	positive regulation of endocytosis	0.0268120729752947
GO:0012510	trans-Golgi network transport vesicle membrane	0.0268120729752947
GO:0030159	receptor signaling complex scaffold activity	0.0268120729752947
GO:0017124	SH3 domain binding	0.0277325453196628
GO:0032947	protein complex scaffold	0.0277325453196628
GO:0030125	clathrin vesicle coat	0.0280204918071434
GO:0030139	endocytic vesicle	0.0280204918071434
GO:0005829	cytosol	0.0280204918071434
GO:0030665	clathrin coated vesicle membrane	0.0280204918071434
GO:0051098	regulation of binding	0.0330964323601507
GO:0030140	trans-Golgi network transport vesicle	0.0332966133538596
GO:0030658	transport vesicle membrane	0.0338330086151013
GO:0065009	regulation of a molecular function	0.0338330086151013
GO:0030660	Golgi-associated vesicle membrane	0.0338330086151013
GO:0030100	regulation of endocytosis	0.0341451676617017
GO:0005925	focal adhesion	0.0341451676617017
GO:0007292	female gamete generation	0.03428961072765
GO:0005924	cell-substrate adherens junction	0.0350245552621578
GO:0051050	positive regulation of transport	0.0350245552621578
GO:0030027	lamellipodium	0.0350245552621578
GO:0030055	cell-matrix junction	0.0350245552621578
GO:0007015	actin filament organization	0.0350245552621578
GO:0006898	receptor-mediated endocytosis	0.0350245552621578
GO:0005905	coated pit	0.0359625052134099
GO:0006919	caspase activation	0.0376780663092173
GO:0051052	regulation of DNA metabolic process	0.0378523782391324
GO:0005769	early endosome	0.0378523782391324
GO:0030120	vesicle coat	0.0378523782391324
GO:0043280	positive regulation of caspase activity	0.0378523782391324
GO:0030662	coated vesicle membrane	0.0378916483779762
GO:0030131	clathrin adaptor complex	0.0380005712279603
GO:0005912	adherens junction	0.0380005712279603
GO:0030119	AP-type membrane coat adaptor complex	0.0380005712279603
GO:0043281	regulation of caspase activity	0.0414500800115022
GO:0008154	actin polymerization and/or depolymerization	0.0414500800115022
GO:0030133	transport vesicle	0.0420894203107372
GO:0030118	clathrin coat	0.0433612596610362
GO:0005798	Golgi-associated vesicle	0.0445912181473384
GO:0031252	leading edge	0.04507972218143
GO:0012505	endomembrane system	0.04507972218143
GO:0008022	protein C-terminus binding	0.0455984987589061
GO:0051345	positive regulation of hydrolase activity	0.0461145460520442
GO:0008203	cholesterol metabolic process	0.0466148382190784
GO:0043229	intracellular organelle	0.0466526491276922
GO:0043226	organelle	0.0466526491276922
GO:0016043	cellular component organization and biogenesis	0.0467027924574183

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
lymphocyte	5.60e-13	53
common lymphoid progenitor	5.60e-13	53
lymphoid lineage restricted progenitor cell	1.74e-12	52
lymphocyte of B lineage	3.30e-12	24
pro-B cell	3.30e-12	24
hematopoietic stem cell	1.35e-08	172
angioblastic mesenchymal cell	1.35e-08	172
hematopoietic cell	2.07e-08	182
hematopoietic oligopotent progenitor cell	1.09e-07	165
hematopoietic multipotent progenitor cell	1.09e-07	165

Uber Anatomy

Ontology term	p-value	n
adult organism	4.70e-10	115
neural tube	1.89e-07	57
neural rod	1.89e-07	57
future spinal cord	1.89e-07	57
neural keel	1.89e-07	57

Disease

Ontology term	p-value	n
cancer	8.31e-12	235
hematologic cancer	4.16e-11	51
immune system cancer	4.16e-11	51
disease of cellular proliferation	5.04e-11	239
organ system cancer	3.42e-09	137
cell type cancer	4.99e-07	143
lymphoma	5.80e-07	10

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
EBF1#1879	22	1.90235214198561	0.00219295821888588	0.0126403423711144

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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