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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 10:46, 17 September 2013


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)
MA0003.10.0238818
MA0004.11.87237
MA0006.10.0227073
MA0007.10.410725
MA0009.10.621204
MA0014.10.00110159
MA0017.11.43991
MA0019.11.81456
MA0024.10.191942
MA0025.10.152426
MA0027.11.42172
MA0028.10.000720034
MA0029.10.0576109
MA0030.10.769025
MA0031.11.82571
MA0038.10.591021
MA0040.10.0595103
MA0041.10.532398
MA0042.10.427129
MA0043.10.0890602
MA0046.11.0083
MA0048.10.514675
MA0050.10.624672
MA0051.10.83837
MA0052.10.060786
MA0055.10.464878
MA0056.10
MA0057.10.0132315
MA0058.12.00109
MA0059.10.859899
MA0060.10.017433
MA0061.10.0306789
MA0063.10
MA0066.11.16959
MA0067.10.265212
MA0068.10.00891545
MA0069.10.282463
MA0070.10.570402
MA0071.10.070072
MA0072.10.0769043
MA0073.19.89496e-13
MA0074.11.49029
MA0076.10.00284478
MA0077.10.930101
MA0078.10.928097
MA0081.10.0615144
MA0083.10.0920437
MA0084.10.403089
MA0087.10.262908
MA0088.10.41335
MA0089.10
MA0090.10.425247
MA0091.10.0369142
MA0092.11.26637
MA0093.12.59657
MA0095.10
MA0098.10
MA0100.10.109898
MA0101.10.392603
MA0103.15.20698
MA0105.10.0129476
MA0106.10.0097114
MA0107.10.0287337
MA0108.20.0354454
MA0109.10
MA0111.10.315932
MA0113.10.0559966
MA0114.12.69888
MA0115.11.80947
MA0116.10.0592594
MA0117.10.342325
MA0119.15.0467
MA0122.10.117023
MA0124.10.189889
MA0125.12.01048
MA0130.10
MA0131.10.412002
MA0132.10
MA0133.10
MA0135.10.682662
MA0136.10.391616
MA0139.10.384419
MA0140.10.688815
MA0141.10.463488
MA0142.10.287194
MA0143.10.0560768
MA0144.10.252922
MA0145.10.0762155
MA0146.10.133573
MA0147.11.00357
MA0148.11.71262
MA0149.10.0032556
MA0062.20.00638472
MA0035.20.284341
MA0039.20.0525706
MA0138.20.19388
MA0002.20.582504
MA0137.20.211673
MA0104.21.00766
MA0047.22.13461
MA0112.20.470474
MA0065.20.262975
MA0150.10.78451
MA0151.10
MA0152.10.483435
MA0153.10.418129
MA0154.10.251601
MA0155.10.788717
MA0156.10.329348
MA0157.10.469246
MA0158.10
MA0159.11.00943
MA0160.11.14437
MA0161.10
MA0162.10.00391803
MA0163.10.00417782
MA0164.10.552256
MA0080.20.379885
MA0018.20.136257
MA0099.20.991569
MA0079.24.45519e-14
MA0102.20.432633
MA0258.11.25978
MA0259.10.124544
MA0442.10



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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