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Coexpression cluster:C164

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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

p.valueFDRnGenesnPathwayName
4.36525441512756e-050.0276320604477574226Glycosphingolipid 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

GO IDGO nameFDR corrected p-value
GO:0016020membrane0.0183789192023041
GO:0015349thyroid hormone transmembrane transporter activity0.0183789192023041
GO:0005794Golgi apparatus0.0183789192023041
GO:0044425membrane part0.0183789192023041
GO:0003836beta-galactoside alpha-2,3-sialyltransferase activity0.0183789192023041
GO:00170603-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity0.0183789192023041
GO:0006486protein amino acid glycosylation0.0183789192023041
GO:0043413biopolymer glycosylation0.0183789192023041
GO:0009101glycoprotein biosynthetic process0.0183789192023041
GO:0009100glycoprotein metabolic process0.0215423688148316
GO:0005007fibroblast growth factor receptor activity0.0238291314514662
GO:0030036actin cytoskeleton organization and biogenesis0.0251988738410542
GO:0030029actin filament-based process0.0257325898940194
GO:0008091spectrin0.0300468781743587
GO:0016021integral to membrane0.0300468781743587
GO:0031224intrinsic to membrane0.0300468781743587
GO:0042403thyroid hormone metabolic process0.0308159227744796
GO:0044444cytoplasmic part0.0316174475128146
GO:0006464protein modification process0.0316174475128146
GO:0043412biopolymer modification0.033245971649404
GO:0030864cortical actin cytoskeleton0.033245971649404
GO:0008417fucosyltransferase activity0.0356932355082244
GO:0051693actin filament capping0.0358137908409585
GO:0051016barbed-end actin filament capping0.0358137908409585
GO:0016757transferase activity, transferring glycosyl groups0.0358137908409585
GO:0030835negative regulation of actin filament depolymerization0.0358137908409585
GO:0030834regulation of actin filament depolymerization0.0358137908409585
GO:0030042actin filament depolymerization0.0358137908409585
GO:0030863cortical cytoskeleton0.0375768407342354
GO:0016740transferase activity0.0397882644831204
GO:0044267cellular protein metabolic process0.0447879837481567
GO:0044260cellular macromolecule metabolic process0.045888328141626



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>

Cell Type
Ontology termp-valuen
epithelial cell of stomach2.39e-663
epithelial cell of alimentary canal2.29e-1120
Uber Anatomy
Ontology termp-valuen
stomach5.22e-268
food storage organ5.22e-268
gastrointestinal system4.34e-0925
Disease
Ontology termp-valuen
signet ring cell adenocarcinoma1.55e-982
gastrointestinal system cancer1.43e-1514
adenocarcinoma2.15e-0925


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

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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BHLHE40#855383.418804841674470.002492330496741090.0139951881686727
ESR1#2099102.930343171062330.002277034521151650.0129266297958665
FOXA2#3170102.345758452634790.01049821323574570.0388733519634124



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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