Coexpression cluster:C164

Full id: C164_signet_corpus_optic_mucinous_substantia_salivary_choriocarcinoma

Phase1 CAGE Peaks

Hg19::chr10:122520831..122520842,+	p@chr10:122520831..122520842 +
Hg19::chr10:122520854..122520858,+	p@chr10:122520854..122520858 +
Hg19::chr10:122520908..122520928,+	p@chr10:122520908..122520928 +
Hg19::chr10:122521149..122521164,+	p@chr10:122521149..122521164 +
Hg19::chr10:122907103..122907107,+	p@chr10:122907103..122907107 +
Hg19::chr10:122910650..122910656,+	p@chr10:122910650..122910656 +
Hg19::chr10:123000012..123000015,+	p@chr10:123000012..123000015 +
Hg19::chr10:123274755..123274769,-	p9@FGFR2
Hg19::chr10:123305695..123305700,-	p@chr10:123305695..123305700 -
Hg19::chr10:123310876..123310882,-	p@chr10:123310876..123310882 -
Hg19::chr10:123313149..123313152,+	p@chr10:123313149..123313152 +
Hg19::chr10:123324686..123324691,-	p@chr10:123324686..123324691 -
Hg19::chr10:123325052..123325063,-	p13@FGFR2
Hg19::chr10:123357874..123357895,-	p2@FGFR2
Hg19::chr10:123357913..123357975,-	p1@FGFR2
Hg19::chr10:123357978..123357984,-	p7@FGFR2
Hg19::chr10:123378808..123378819,-	p@chr10:123378808..123378819 -
Hg19::chr10:123378848..123378857,-	p@chr10:123378848..123378857 -
Hg19::chr10:29217713..29217810,+	p@chr10:29217713..29217810 +
Hg19::chr10:29217811..29217823,+	p@chr10:29217811..29217823 +
Hg19::chr10:29217837..29217846,+	p@chr10:29217837..29217846 +
Hg19::chr10:29217861..29217870,+	p@chr10:29217861..29217870 +
Hg19::chr11:126275925..126275951,+	p6@ST3GAL4
Hg19::chr11:126275956..126275992,+	p2@ST3GAL4
Hg19::chr13:107028964..107028978,+	p2@LINC00460
Hg19::chr13:107029290..107029313,+	p3@LINC00460
Hg19::chr13:113677114..113677156,-	p@chr13:113677114..113677156 -
Hg19::chr13:113677163..113677183,-	p@chr13:113677163..113677183 -
Hg19::chr13:113719222..113719233,+	p@chr13:113719222..113719233 +
Hg19::chr13:113719247..113719258,+	p@chr13:113719247..113719258 +
Hg19::chr13:113719825..113719834,-	p@chr13:113719825..113719834 -
Hg19::chr13:73809919..73809926,+	p@chr13:73809919..73809926 +
Hg19::chr13:97775112..97775117,+	p@chr13:97775112..97775117 +
Hg19::chr13:97775142..97775154,+	p@chr13:97775142..97775154 +
Hg19::chr15:42186162..42186197,-	p1@SPTBN5
Hg19::chr15:42186200..42186205,-	p3@SPTBN5
Hg19::chr15:42186211..42186222,-	p2@SPTBN5
Hg19::chr15:42186248..42186253,-	p4@SPTBN5
Hg19::chr17:70053866..70053882,-	p1@ENST00000424417 p1@ENST00000540802
Hg19::chr17:70619903..70619909,+	p@chr17:70619903..70619909 +
Hg19::chr17:79433064..79433096,-	p@chr17:79433064..79433096 -
Hg19::chr19:10142077..10142083,-	p@chr19:10142077..10142083 -
Hg19::chr19:10142089..10142103,-	p@chr19:10142089..10142103 -
Hg19::chr19:10142279..10142292,-	p@chr19:10142279..10142292 -
Hg19::chr19:51472686..51472697,-	p@chr19:51472686..51472697 -
Hg19::chr19:5846627..5846646,-	p4@FUT3
Hg19::chr19:5846676..5846682,-	p7@FUT3
Hg19::chr1:154306439..154306461,+	p@chr1:154306439..154306461 +
Hg19::chr1:3240057..3240066,-	p@chr1:3240057..3240066 -
Hg19::chr20:61278219..61278228,-	p@chr20:61278219..61278228 -
Hg19::chr20:61298173..61298178,-	p4@ENST00000411824
Hg19::chr20:61298207..61298221,-	p2@ENST00000411824
Hg19::chr20:61298260..61298263,-	p3@ENST00000411824
Hg19::chr20:61298271..61298272,-	p5@ENST00000411824
Hg19::chr20:61298826..61298834,+	p13@SLCO4A1
Hg19::chr20:61299085..61299091,+	p24@SLCO4A1
Hg19::chr20:61299155..61299169,+	p10@SLCO4A1
Hg19::chr20:61316967..61316974,-	p@chr20:61316967..61316974 -
Hg19::chr20:61317513..61317519,-	p@chr20:61317513..61317519 -
Hg19::chr20:61368258..61368275,+	p@chr20:61368258..61368275 +
Hg19::chr20:61368291..61368301,+	p@chr20:61368291..61368301 +
Hg19::chr21:36061591..36061600,+	p@chr21:36061591..36061600 +
Hg19::chr21:43767753..43767789,-	p@chr21:43767753..43767789 -
Hg19::chr22:43343242..43343291,-	p20@PACSIN2
Hg19::chr22:46406849..46406852,+	p@chr22:46406849..46406852 +
Hg19::chr22:49239060..49239068,+	p@chr22:49239060..49239068 +
Hg19::chr2:113483733..113483750,+	p3@NT5DC4
Hg19::chr2:121082746..121082759,-	p@chr2:121082746..121082759 -
Hg19::chr2:176343442..176343471,+	p@chr2:176343442..176343471 +
Hg19::chr2:236405138..236405159,-	p@chr2:236405138..236405159 -
Hg19::chr2:28762016..28762055,-	p@chr2:28762016..28762055 -
Hg19::chr2:37609861..37609884,+	p@chr2:37609861..37609884 +
Hg19::chr2:37611635..37611676,-	p@chr2:37611635..37611676 -
Hg19::chr2:9324969..9324972,-	p@chr2:9324969..9324972 -
Hg19::chr3:124209926..124209941,-	p@chr3:124209926..124209941 -
Hg19::chr3:41238327..41238331,+	p@chr3:41238327..41238331 +
Hg19::chr4:909521..909534,-	p5@GAK
Hg19::chr4:909539..909550,-	p7@GAK
Hg19::chr5:123739068..123739080,-	p@chr5:123739068..123739080 -
Hg19::chr5:123739189..123739215,+	p@chr5:123739189..123739215 +
Hg19::chr5:123739217..123739231,+	p@chr5:123739217..123739231 +
Hg19::chr5:167545081..167545101,+	p46@ODZ2
Hg19::chr5:167545123..167545128,+	p60@ODZ2
Hg19::chr5:167545165..167545170,+	p61@ODZ2
Hg19::chr5:496367..496402,-	p@chr5:496367..496402 -
Hg19::chr5:498417..498421,-	p@chr5:498417..498421 -
Hg19::chr5:499767..499777,-	p@chr5:499767..499777 -
Hg19::chr5:499786..499794,-	p@chr5:499786..499794 -
Hg19::chr6:110282878..110282882,-	p@chr6:110282878..110282882 -
Hg19::chr6:167684529..167684536,+	p6@UNC93A
Hg19::chr6:167684651..167684669,+	p1@UNC93A
Hg19::chr6:167684810..167684828,+	p2@UNC93A
Hg19::chr6:167684834..167684837,+	p7@UNC93A
Hg19::chr7:36324273..36324284,+	p@chr7:36324273..36324284 +
Hg19::chr7:36324296..36324314,+	p@chr7:36324296..36324314 +
Hg19::chr7:73062013..73062025,-	p@chr7:73062013..73062025 -
Hg19::chr7:960476..960493,-	p11@ADAP1
Hg19::chr7:960494..960498,-	p19@ADAP1
Hg19::chr8:125639273..125639286,+	p@chr8:125639273..125639286 +
Hg19::chr8:22773017..22773028,-	p@chr8:22773017..22773028 -
Hg19::chr9:130913070..130913089,+	p@chr9:130913070..130913089 +
Hg19::chr9:130913151..130913159,+	p@chr9:130913151..130913159 +
Hg19::chr9:130913176..130913179,+	p@chr9:130913176..130913179 +
Hg19::chr9:133822857..133822869,-	p@chr9:133822857..133822869 -
Hg19::chr9:133822880..133822891,-	p@chr9:133822880..133822891 -

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
4.36525441512756e-05	0.0276320604477574	2	26	Glycosphingolipid biosynthesis - lacto and neolacto series (KEGG):00601

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:0016020	membrane	0.0183789192023041
GO:0015349	thyroid hormone transmembrane transporter activity	0.0183789192023041
GO:0005794	Golgi apparatus	0.0183789192023041
GO:0044425	membrane part	0.0183789192023041
GO:0003836	beta-galactoside alpha-2,3-sialyltransferase activity	0.0183789192023041
GO:0017060	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity	0.0183789192023041
GO:0006486	protein amino acid glycosylation	0.0183789192023041
GO:0043413	biopolymer glycosylation	0.0183789192023041
GO:0009101	glycoprotein biosynthetic process	0.0183789192023041
GO:0009100	glycoprotein metabolic process	0.0215423688148316
GO:0005007	fibroblast growth factor receptor activity	0.0238291314514662
GO:0030036	actin cytoskeleton organization and biogenesis	0.0251988738410542
GO:0030029	actin filament-based process	0.0257325898940194
GO:0008091	spectrin	0.0300468781743587
GO:0016021	integral to membrane	0.0300468781743587
GO:0031224	intrinsic to membrane	0.0300468781743587
GO:0042403	thyroid hormone metabolic process	0.0308159227744796
GO:0044444	cytoplasmic part	0.0316174475128146
GO:0006464	protein modification process	0.0316174475128146
GO:0043412	biopolymer modification	0.033245971649404
GO:0030864	cortical actin cytoskeleton	0.033245971649404
GO:0008417	fucosyltransferase activity	0.0356932355082244
GO:0051693	actin filament capping	0.0358137908409585
GO:0051016	barbed-end actin filament capping	0.0358137908409585
GO:0016757	transferase activity, transferring glycosyl groups	0.0358137908409585
GO:0030835	negative regulation of actin filament depolymerization	0.0358137908409585
GO:0030834	regulation of actin filament depolymerization	0.0358137908409585
GO:0030042	actin filament depolymerization	0.0358137908409585
GO:0030863	cortical cytoskeleton	0.0375768407342354
GO:0016740	transferase activity	0.0397882644831204
GO:0044267	cellular protein metabolic process	0.0447879837481567
GO:0044260	cellular macromolecule metabolic process	0.045888328141626

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
endodermal cell	1.26e-08	59
epithelial cell	4.03e-08	254
endo-epithelial cell	2.90e-07	43

Uber Anatomy

Ontology term	p-value	n
adult organism	3.26e-29	115
central nervous system	1.04e-22	82
neural tube	1.24e-21	57
neural rod	1.24e-21	57
future spinal cord	1.24e-21	57
neural keel	1.24e-21	57
organ	5.68e-20	511
regional part of nervous system	5.77e-20	94
nervous system	5.77e-20	94
ectoderm-derived structure	2.27e-19	169
ectoderm	2.04e-18	173
presumptive ectoderm	2.04e-18	173
brain	2.05e-18	69
future brain	2.05e-18	69
regional part of brain	6.49e-18	59
anterior region of body	2.03e-17	129
craniocervical region	2.03e-17	129
head	5.45e-17	123
anterior neural tube	6.33e-16	42
regional part of forebrain	1.07e-15	41
forebrain	1.07e-15	41
future forebrain	1.07e-15	41
neural plate	4.03e-15	86
presumptive neural plate	4.03e-15	86
gray matter	1.59e-14	34
brain grey matter	1.59e-14	34
telencephalon	1.62e-14	34
regional part of telencephalon	4.48e-14	33
neurectoderm	7.30e-14	90
endoderm-derived structure	7.40e-14	169
endoderm	7.40e-14	169
presumptive endoderm	7.40e-14	169
organ part	2.14e-13	219
cerebral hemisphere	2.34e-13	32
digestive system	4.33e-13	155
digestive tract	4.33e-13	155
primitive gut	4.33e-13	155
multi-cellular organism	2.68e-12	659
embryo	3.41e-12	612
subdivision of digestive tract	9.42e-12	129
endodermal part of digestive tract	9.42e-12	129
pre-chordal neural plate	2.58e-11	61
mixed endoderm/mesoderm-derived structure	1.12e-10	130
organism subdivision	2.16e-10	365
anatomical system	2.70e-10	625
cerebral cortex	2.82e-10	25
pallium	2.82e-10	25
embryonic structure	3.68e-10	605
developing anatomical structure	3.68e-10	605
anatomical group	5.18e-10	626
multi-tissue structure	6.99e-10	347
germ layer	7.52e-10	604
embryonic tissue	7.52e-10	604
presumptive structure	7.52e-10	604
epiblast (generic)	7.52e-10	604
regional part of cerebral cortex	8.49e-10	22
neocortex	3.68e-09	20
foregut	3.80e-09	98
respiratory system	4.07e-07	72
immaterial anatomical entity	4.99e-07	126
posterior neural tube	5.91e-07	15
chordal neural plate	5.91e-07	15

Disease

Ontology term	p-value	n
carcinoma	2.73e-16	106
cell type cancer	2.47e-13	143

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	8	3.41880484167447	0.00249233049674109	0.0139951881686727
ESR1#2099	10	2.93034317106233	0.00227703452115165	0.0129266297958665
FOXA2#3170	10	2.34575845263479	0.0104982132357457	0.0388733519634124

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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