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

Latest revision as of 10:45, 17 September 2013


Full id: C159_choriocarcinoma_pancreatic_placenta_chorionic_testicular_bronchioalveolar_seminal



Phase1 CAGE Peaks

Hg19::chr10:114437568..114437582,-p1@ENST00000443652
Hg19::chr10:134217889..134217902,+p12@PWWP2B
Hg19::chr10:79617081..79617125,-p@chr10:79617081..79617125
-
Hg19::chr10:79617136..79617150,-p@chr10:79617136..79617150
-
Hg19::chr10:79617159..79617171,-p@chr10:79617159..79617171
-
Hg19::chr10:79617174..79617179,-p@chr10:79617174..79617179
-
Hg19::chr10:79617215..79617226,-p@chr10:79617215..79617226
-
Hg19::chr10:8223647..8223685,-p@chr10:8223647..8223685
-
Hg19::chr11:18960954..18960967,-p1@MRGPRX1
Hg19::chr11:18961040..18961073,-p2@MRGPRX1
Hg19::chr11:6281059..6281104,+p1@CCKBR
Hg19::chr12:15082050..15082081,-p1@ERP27
Hg19::chr13:78505877..78505880,-p@chr13:78505877..78505880
-
Hg19::chr14:104638084..104638094,+p@chr14:104638084..104638094
+
Hg19::chr14:62585332..62585337,+p2@ENST00000554895
Hg19::chr14:62585350..62585362,+p1@ENST00000554895
Hg19::chr14:62585418..62585425,+p3@ENST00000554895
Hg19::chr14:96968802..96968817,+p2@PAPOLA
Hg19::chr15:52497258..52497274,-p@chr15:52497258..52497274
-
Hg19::chr15:52497278..52497279,-p@chr15:52497278..52497279
-
Hg19::chr15:59243695..59243703,-p@chr15:59243695..59243703
-
Hg19::chr15:91072855..91072876,+p8@CRTC3
Hg19::chr15:96607616..96607625,-p3@ENST00000558860
Hg19::chr15:96833987..96834012,-p@chr15:96833987..96834012
-
Hg19::chr15:96869511..96869525,+p16@NR2F2
Hg19::chr16:89971162..89971177,+p@chr16:89971162..89971177
+
Hg19::chr16:89971202..89971207,+p@chr16:89971202..89971207
+
Hg19::chr16:89971221..89971231,+p@chr16:89971221..89971231
+
Hg19::chr17:45928521..45928539,-p1@SP6
Hg19::chr17:63533845..63533851,-p@chr17:63533845..63533851
-
Hg19::chr17:63533919..63533920,-p@chr17:63533919..63533920
-
Hg19::chr17:63533962..63533988,-p@chr17:63533962..63533988
-
Hg19::chr17:63533993..63534003,-p@chr17:63533993..63534003
-
Hg19::chr19:24346270..24346279,-p2@LOC100101266
Hg19::chr19:39627378..39627388,+p@chr19:39627378..39627388
+
Hg19::chr19:48977067..48977088,+p@chr19:48977067..48977088
+
Hg19::chr19:51267068..51267083,+p@chr19:51267068..51267083
+
Hg19::chr19:54198538..54198542,+p1@MIR519B
Hg19::chr19:54231988..54231990,+p@chr19:54231988..54231990
+
Hg19::chr19:884972..884979,-p@chr19:884972..884979
-
Hg19::chr19:884982..884988,-p@chr19:884982..884988
-
Hg19::chr19:884994..885014,-p@chr19:884994..885014
-
Hg19::chr19:929006..929018,+p14@ARID3A
Hg19::chr19:929027..929051,+p4@ARID3A
Hg19::chr1:146989697..146989701,-p1@LOC100289211
Hg19::chr1:172648770..172648783,+p@chr1:172648770..172648783
+
Hg19::chr1:172648801..172648806,+p@chr1:172648801..172648806
+
Hg19::chr1:200877847..200877851,+p@chr1:200877847..200877851
+
Hg19::chr1:200877866..200877876,+p@chr1:200877866..200877876
+
Hg19::chr1:2021518..2021526,-p@chr1:2021518..2021526
-
Hg19::chr1:229087653..229087688,-p@chr1:229087653..229087688
-
Hg19::chr1:26686541..26686559,-p@chr1:26686541..26686559
-
Hg19::chr1:26686590..26686595,-p@chr1:26686590..26686595
-
Hg19::chr20:55563221..55563236,+p@chr20:55563221..55563236
+
Hg19::chr21:19117606..19117619,+p@chr21:19117606..19117619
+
Hg19::chr22:26106667..26106674,+p@chr22:26106667..26106674
+
Hg19::chr2:11251843..11251854,-p@chr2:11251843..11251854
-
Hg19::chr2:11251855..11251865,-p@chr2:11251855..11251865
-
Hg19::chr2:11251872..11251879,-p@chr2:11251872..11251879
-
Hg19::chr2:16067839..16067847,-p@chr2:16067839..16067847
-
Hg19::chr2:16067860..16067865,-p@chr2:16067860..16067865
-
Hg19::chr2:163101340..163101352,-p7@FAP
Hg19::chr2:16504272..16504306,+p@chr2:16504272..16504306
+
Hg19::chr2:16504345..16504381,+p@chr2:16504345..16504381
+
Hg19::chr2:172087828..172087839,-p20@TLK1
Hg19::chr2:192456035..192456041,+p@chr2:192456035..192456041
+
Hg19::chr2:242913327..242913332,+p1@ENST00000426962
Hg19::chr2:41605365..41605372,+p@chr2:41605365..41605372
+
Hg19::chr2:46656327..46656345,+p3@LOC388946
Hg19::chr2:46656347..46656363,+p2@LOC388946
Hg19::chr2:46669579..46669581,+p@chr2:46669579..46669581
+
Hg19::chr2:46682317..46682319,+p@chr2:46682317..46682319
+
Hg19::chr2:71277301..71277315,+p@chr2:71277301..71277315
+
Hg19::chr2:71277316..71277323,+p@chr2:71277316..71277323
+
Hg19::chr2:71277325..71277344,+p@chr2:71277325..71277344
+
Hg19::chr2:88803506..88803509,+p@chr2:88803506..88803509
+
Hg19::chr2:97535773..97535843,-p1@SEMA4C
Hg19::chr3:195581080..195581110,-p1@ENST00000444346
Hg19::chr3:87174378..87174403,-p@chr3:87174378..87174403
-
Hg19::chr4:106135812..106135817,+p@chr4:106135812..106135817
+
Hg19::chr4:176372622..176372659,-p@chr4:176372622..176372659
-
Hg19::chr4:183164566..183164573,+p14@ODZ3
Hg19::chr4:183164574..183164586,+p8@ODZ3
Hg19::chr4:189027159..189027178,-p4@TRIML2
Hg19::chr4:189064784..189064793,+p1@TRIML1
Hg19::chr4:8582132..8582151,+p3@GPR78
Hg19::chr5:16897687..16897692,-p@chr5:16897687..16897692
-
Hg19::chr5:172721751..172721762,-p2@ENST00000501670
Hg19::chr5:172721766..172721775,-p3@ENST00000501670
Hg19::chr5:39220845..39220852,-p@chr5:39220845..39220852
-
Hg19::chr5:70868039..70868044,+p@chr5:70868039..70868044
+
Hg19::chr6:148501038..148501057,-p@chr6:148501038..148501057
-
Hg19::chr6:25218773..25218788,-p10@CMAHP
Hg19::chr6:56258939..56258948,-p8@COL21A1
Hg19::chr6:56258957..56258965,-p10@COL21A1
Hg19::chr6:90213624..90213631,+p@chr6:90213624..90213631
+
Hg19::chr7:107643964..107643973,-p10@LAMB1
Hg19::chr7:12628967..12628976,+p6@SCIN
Hg19::chr7:134932245..134932256,-p@chr7:134932245..134932256
-
Hg19::chr7:2883766..2883775,-p7@GNA12
Hg19::chr8:135708824..135708829,-p24@ZFAT
Hg19::chr9:134585127..134585165,-p7@RAPGEF1
Hg19::chrX:49819025..49819038,+p@chrX:49819025..49819038
+
Hg19::chrX:49819043..49819049,+p@chrX:49819043..49819049
+
Hg19::chrX:49819053..49819064,+p@chrX:49819053..49819064
+
Hg19::chrX:56058051..56058060,-p@chrX:56058051..56058060
-
Hg19::chrX:62654223..62654277,-p@chrX:62654223..62654277
-
Hg19::chrX:62654282..62654291,-p@chrX:62654282..62654291
-
Hg19::chrX:7137573..7137574,+p19@STS


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

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

GO IDGO nameFDR corrected p-value
GO:0004773steryl-sulfatase activity0.0374720357941834
GO:0045654positive regulation of megakaryocyte differentiation0.0374720357941834
GO:0043257laminin-8 complex0.0374720357941834
GO:0005607laminin-2 complex0.0374720357941834
GO:0009956radial pattern formation0.0374720357941834
GO:00469351-phosphatidylinositol-3-kinase regulator activity0.0374720357941834
GO:0015054gastrin receptor activity0.0408677544635792
GO:0001672regulation of chromatin assembly or disassembly0.0408677544635792
GO:0045652regulation of megakaryocyte differentiation0.0408677544635792
GO:0045010actin nucleation0.0408677544635792
GO:0043259laminin-10 complex0.0408677544635792
GO:0051128regulation of cellular component organization and biogenesis0.0449426208413752
GO:0048731system development0.0449426208413752
GO:0004951cholecystokinin receptor activity0.0449426208413752
GO:0030219megakaryocyte differentiation0.0449426208413752



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
germ line cell4.35e-377
germ cell4.35e-377
epithelial cell of pancreas1.96e-084
Uber Anatomy
Ontology termp-valuen
placenta2.11e-084
allantois2.11e-084


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)
MA0003.10.201519
MA0004.10.00848347
MA0006.11.23075
MA0007.10.232841
MA0009.10.591368
MA0014.12.18607e-06
MA0017.11.07713
MA0019.10.450068
MA0024.10.178643
MA0025.10.144229
MA0027.11.4058
MA0028.10.100475
MA0029.10.195976
MA0030.10.730004
MA0031.11.29477
MA0038.10.344138
MA0040.10.444381
MA0041.10.699697
MA0042.10.387269
MA0043.12.04005
MA0046.10.0786003
MA0048.10.34518
MA0050.10.0260629
MA0051.10.534321
MA0052.10.451122
MA0055.10.0408078
MA0056.10
MA0057.10.00897299
MA0058.10.00726369
MA0059.10.0517527
MA0060.11.28969
MA0061.10.107405
MA0063.10
MA0066.11.43809
MA0067.10.2546
MA0068.10.00114605
MA0069.10.0771311
MA0070.10.541654
MA0071.10.64729
MA0072.10.533205
MA0073.11.88052e-07
MA0074.10.0839539
MA0076.10.216253
MA0077.10.518838
MA0078.10.581654
MA0081.10.180622
MA0083.12.07524
MA0084.10.390659
MA0087.10.0704249
MA0088.10.679554
MA0089.10
MA0090.12.56671
MA0091.10.43611
MA0092.10.912928
MA0093.10.000380619
MA0095.10
MA0098.10
MA0100.10.591115
MA0101.10.0455525
MA0103.10.291487
MA0105.10.215388
MA0106.10.440427
MA0107.10.0225395
MA0108.20.307704
MA0109.10
MA0111.10.0919968
MA0113.10.280652
MA0114.11.41806
MA0115.10.593126
MA0116.11.07078
MA0117.10.324405
MA0119.10.514564
MA0122.10.719742
MA0124.10.180752
MA0125.10.135009
MA0130.10
MA0131.10.0167544
MA0132.10
MA0133.10
MA0135.10.651619
MA0136.10.359808
MA0139.10.0158068
MA0140.12.29672
MA0141.10.281385
MA0142.10.266706
MA0143.11.04773
MA0144.10.854395
MA0145.10.189376
MA0146.10.164194
MA0147.10.00455104
MA0148.10.984952
MA0149.10.0166904
MA0062.20.0951018
MA0035.22.72521
MA0039.20.0560759
MA0138.20.350169
MA0002.21.13935
MA0137.20.409825
MA0104.20.000699262
MA0047.21.24792
MA0112.20.0595443
MA0065.20.928452
MA0150.10.942023
MA0151.10
MA0152.10.271835
MA0153.10.126593
MA0154.11.44331
MA0155.10.1208
MA0156.10.419058
MA0157.10.438272
MA0158.10
MA0159.10.221517
MA0160.10.369239
MA0161.10
MA0162.10.0466837
MA0163.10.000771133
MA0164.10.302268
MA0080.20.143622
MA0018.22.13107
MA0099.20.146184
MA0079.22.32795e-11
MA0102.20.419911
MA0258.10.122239
MA0259.10.473954
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
GATA3#2625143.498268155971414.82570150565378e-050.000838867242924392



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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