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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: C163_Skeletal_skeletal_Pericytes_Hepatic_rhabdomyosarcoma_throat_mesenchymal



Phase1 CAGE Peaks

Hg19::chr10:14413956..14413970,+p@chr10:14413956..14413970
+
Hg19::chr10:35701864..35701875,+p@chr10:35701864..35701875
+
Hg19::chr10:35894264..35894279,+p2@GJD4
Hg19::chr10:35894364..35894370,+p4@GJD4
Hg19::chr11:19864352..19864364,+p@chr11:19864352..19864364
+
Hg19::chr11:27216669..27216680,-p@chr11:27216669..27216680
-
Hg19::chr11:44884533..44884555,+p@chr11:44884533..44884555
+
Hg19::chr11:71903281..71903288,+p8@FOLR1
Hg19::chr11:85090268..85090294,-p@chr11:85090268..85090294
-
Hg19::chr12:106452212..106452215,-p1@ENST00000546699
Hg19::chr12:109967979..109967983,+p@chr12:109967979..109967983
+
Hg19::chr12:123356789..123356800,-p2@AK123249
Hg19::chr12:123356838..123356845,-p3@AK123249
Hg19::chr12:56548421..56548450,+p@chr12:56548421..56548450
+
Hg19::chr12:77260043..77260058,-p5@CSRP2
Hg19::chr12:77260065..77260070,-p11@CSRP2
Hg19::chr12:77260073..77260082,-p4@CSRP2
Hg19::chr12:77260106..77260118,-p8@CSRP2
Hg19::chr12:77972314..77972326,-p@chr12:77972314..77972326
-
Hg19::chr13:106582200..106582203,+p@chr13:106582200..106582203
+
Hg19::chr13:36766022..36766034,-p@chr13:36766022..36766034
-
Hg19::chr13:36766145..36766151,-p@chr13:36766145..36766151
-
Hg19::chr14:100589461..100589490,+p@chr14:100589461..100589490
+
Hg19::chr14:105932460..105932466,+p@chr14:105932460..105932466
+
Hg19::chr15:69845019..69845027,+p1@ENST00000559029
Hg19::chr16:57788820..57788863,+p@chr16:57788820..57788863
+
Hg19::chr16:69969598..69969610,+p@chr16:69969598..69969610
+
Hg19::chr16:69969667..69969671,+p@chr16:69969667..69969671
+
Hg19::chr16:70732796..70732803,-p@chr16:70732796..70732803
-
Hg19::chr16:70732811..70732824,-p@chr16:70732811..70732824
-
Hg19::chr16:89241500..89241514,+p@chr16:89241500..89241514
+
Hg19::chr17:10558497..10558505,-p11@MYH3
Hg19::chr17:10560452..10560487,-p@chr17:10560452..10560487
-
Hg19::chr17:10581728..10581741,-p@chr17:10581728..10581741
-
Hg19::chr17:10581804..10581839,-p@chr17:10581804..10581839
-
Hg19::chr17:56614865..56614875,-p@chr17:56614865..56614875
-
Hg19::chr17:56614878..56614885,-p@chr17:56614878..56614885
-
Hg19::chr17:80328411..80328426,+p@chr17:80328411..80328426
+
Hg19::chr17:80329638..80329643,+p@chr17:80329638..80329643
+
Hg19::chr17:80329700..80329722,+p@chr17:80329700..80329722
+
Hg19::chr17:80329732..80329753,+p@chr17:80329732..80329753
+
Hg19::chr19:18554702..18554705,-p5@ENST00000541164
Hg19::chr19:19586378..19586389,+p@chr19:19586378..19586389
+
Hg19::chr19:48283768..48283781,+p@chr19:48283768..48283781
+
Hg19::chr19:49659292..49659321,+p@chr19:49659292..49659321
+
Hg19::chr1:117253109..117253129,-p@chr1:117253109..117253129
-
Hg19::chr1:16062820..16062831,+p3@SLC25A34
Hg19::chr1:201399370..201399380,-p8@TNNI1
Hg19::chr1:203036733..203036740,+p@chr1:203036733..203036740
+
Hg19::chr1:203036812..203036840,+p@chr1:203036812..203036840
+
Hg19::chr1:204420108..204420117,-p@chr1:204420108..204420117
-
Hg19::chr1:205210718..205210738,+p@chr1:205210718..205210738
+
Hg19::chr1:33338076..33338105,-p3@FNDC5
Hg19::chr1:36621141..36621167,+p21@MAP7D1
Hg19::chr1:61416169..61416181,-p@chr1:61416169..61416181
-
Hg19::chr1:61418524..61418567,-p1@ENST00000418662
Hg19::chr1:6615391..6615401,+p2@TAS1R1
Hg19::chr1:6615468..6615485,+p1@TAS1R1
Hg19::chr20:52612536..52612547,-p9@BCAS1
Hg19::chr20:52831348..52831363,-p@chr20:52831348..52831363
-
Hg19::chr20:54998100..54998106,+p@chr20:54998100..54998106
+
Hg19::chr20:54998112..54998145,+p@chr20:54998112..54998145
+
Hg19::chr20:54998157..54998168,+p@chr20:54998157..54998168
+
Hg19::chr20:54998171..54998186,+p@chr20:54998171..54998186
+
Hg19::chr20:54998208..54998211,+p@chr20:54998208..54998211
+
Hg19::chr21:44988675..44988677,-p@chr21:44988675..44988677
-
Hg19::chr22:24026365..24026383,-p4@GUSBP11
Hg19::chr22:31489401..31489412,+p38@SMTN
Hg19::chr22:37945945..37945963,+p1@ENST00000428838
Hg19::chr22:46880104..46880107,-p@chr22:46880104..46880107
-
Hg19::chr2:112009644..112009652,+p@chr2:112009644..112009652
+
Hg19::chr2:112009718..112009722,+p@chr2:112009718..112009722
+
Hg19::chr2:145161707..145161728,-p@chr2:145161707..145161728
-
Hg19::chr2:145161747..145161756,-p@chr2:145161747..145161756
-
Hg19::chr2:145161781..145161789,-p@chr2:145161781..145161789
-
Hg19::chr2:233404395..233404408,+p2@CHRNG
Hg19::chr2:39963869..39963884,-p@chr2:39963869..39963884
-
Hg19::chr2:55523476..55523484,-p@chr2:55523476..55523484
-
Hg19::chr2:55523506..55523516,-p@chr2:55523506..55523516
-
Hg19::chr2:55523564..55523568,-p57@CCDC88A
Hg19::chr3:127048582..127048589,-p@chr3:127048582..127048589
-
Hg19::chr3:127048599..127048611,-p@chr3:127048599..127048611
-
Hg19::chr3:165929277..165929294,-p@chr3:165929277..165929294
-
Hg19::chr3:3841142..3841153,+p3@LRRN1
Hg19::chr4:78652737..78652763,-p14@CNOT6L
Hg19::chr5:126737401..126737412,+p@chr5:126737401..126737412
+
Hg19::chr5:131543465..131543475,-p@chr5:131543465..131543475
-
Hg19::chr5:148609626..148609631,+p@chr5:148609626..148609631
+
Hg19::chr5:53776426..53776427,+p@chr5:53776426..53776427
+
Hg19::chr5:53776469..53776484,+p@chr5:53776469..53776484
+
Hg19::chr5:54763740..54763746,-p10@PPAP2A
Hg19::chr5:54763798..54763805,-p9@PPAP2A
Hg19::chr6:31848961..31848968,-p@chr6:31848961..31848968
-
Hg19::chr6:70875603..70875608,+p@chr6:70875603..70875608
+
Hg19::chr6:90378042..90378060,-p@chr6:90378042..90378060
-
Hg19::chr6:90378070..90378073,-p@chr6:90378070..90378073
-
Hg19::chr8:121255414..121255427,+p@chr8:121255414..121255427
+
Hg19::chr8:121255436..121255444,+p@chr8:121255436..121255444
+
Hg19::chr8:121255468..121255505,+p@chr8:121255468..121255505
+
Hg19::chr8:131092296..131092303,-p@chr8:131092296..131092303
-
Hg19::chr8:144799392..144799409,+p@chr8:144799392..144799409
+
Hg19::chr9:14520447..14520460,-p@chr9:14520447..14520460
-
Hg19::chr9:23769271..23769295,-p@chr9:23769271..23769295
-
Hg19::chr9:34311899..34311943,-p6@KIF24
Hg19::chr9:79516011..79516022,-p@chr9:79516011..79516022
-
Hg19::chrX:135827794..135827802,-p@chrX:135827794..135827802
-


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:0003012muscle system process0.000146957112102741
GO:0006936muscle contraction0.000146957112102741
GO:0003779actin binding0.00460640517802088
GO:0007517muscle development0.00535808937720335
GO:0006941striated muscle contraction0.00792418990634807
GO:0008092cytoskeletal protein binding0.00792418990634807
GO:0030017sarcomere0.010423541591481
GO:0030016myofibril0.0110909745475019
GO:0015629actin cytoskeleton0.0110909745475019
GO:0044449contractile fiber part0.0110909745475019
GO:0043292contractile fiber0.0110909745475019
GO:0051179localization0.0110909745475019
GO:0046655folic acid metabolic process0.0110909745475019
GO:0032147activation of protein kinase activity0.0110909745475019
GO:0003008system process0.0114334652383378
GO:0032148activation of protein kinase B0.0164805241120619
GO:0050917sensory perception of umami taste0.0164805241120619
GO:0043422protein kinase B binding0.0164805241120619
GO:0008195phosphatidate phosphatase activity0.0234145219196769
GO:0045860positive regulation of protein kinase activity0.0307058526767125
GO:0033674positive regulation of kinase activity0.0307058526767125
GO:0051347positive regulation of transferase activity0.0307058526767125
GO:0005861troponin complex0.0355665099781149
GO:0015884folic acid transport0.0355665099781149
GO:0008354germ cell migration0.0355665099781149
GO:0005856cytoskeleton0.0383371242852881
GO:0030032lamellipodium biogenesis0.0383371242852881
GO:0006942regulation of striated muscle contraction0.0383371242852881
GO:0004981muscarinic acetylcholine receptor activity0.0383371242852881
GO:0030705cytoskeleton-dependent intracellular transport0.0383371242852881
GO:0007010cytoskeleton organization and biogenesis0.0383371242852881
GO:0008283cell proliferation0.0467847443423427
GO:0051181cofactor transport0.0468106171897425
GO:0005865striated muscle thin filament0.0468106171897425
GO:0016477cell migration0.0468106171897425
GO:0045859regulation of protein kinase activity0.0468106171897425
GO:0043549regulation of kinase activity0.0468106171897425
GO:0005886plasma membrane0.0468106171897425
GO:0051338regulation of transferase activity0.0468106171897425
GO:0032501multicellular organismal process0.0468106171897425
GO:0035091phosphoinositide binding0.0468191190828592
GO:0043085positive regulation of catalytic activity0.047482048231695
GO:0030029actin filament-based process0.0477889462832223
GO:0000146microfilament motor activity0.0479700045599242
GO:0008527taste receptor activity0.0479700045599242
GO:0032982myosin filament0.0479700045599242
GO:0030048actin filament-based movement0.0479700045599242
GO:0051180vitamin transport0.0479700045599242
GO:0005863striated muscle thick filament0.0479700045599242
GO:0016044membrane organization and biogenesis0.0479700045599242
GO:0006810transport0.0479700045599242



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><br>

Uber Anatomy
Ontology termp-valuen
skeletal muscle tissue9.42e-1462
striated muscle tissue9.42e-1462
myotome9.42e-1462
muscle tissue2.45e-1364
musculature2.45e-1364
musculature of body2.45e-1364
somite4.53e-1271
presomitic mesoderm4.53e-1271
presumptive segmental plate4.53e-1271
dermomyotome4.53e-1271
trunk paraxial mesoderm4.53e-1271
paraxial mesoderm6.57e-1272
presumptive paraxial mesoderm6.57e-1272
dense mesenchyme tissue9.42e-1273
epithelial vesicle5.00e-1178
multilaminar epithelium2.17e-1083
trunk mesenchyme3.45e-07122


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)
MA0003.18.16342e-07
MA0004.10.00143918
MA0006.10.00801493
MA0007.10.0701167
MA0009.10.29452
MA0014.12.1629e-06
MA0017.10.152247
MA0019.10.277205
MA0024.10.0504649
MA0025.12.77216
MA0027.11.41768
MA0028.10.0110925
MA0029.10.453649
MA0030.10.19568
MA0031.10.32875
MA0038.10.205758
MA0040.10.211915
MA0041.10.200741
MA0042.10.835792
MA0043.10.614206
MA0046.10.0829948
MA0048.13.64475
MA0050.10.26671
MA0051.10.0922471
MA0052.11.72983
MA0055.111.2391
MA0056.10
MA0057.10.0533037
MA0058.10.00196554
MA0059.10.115391
MA0060.10.0938913
MA0061.10.00293807
MA0063.10
MA0066.10.581154
MA0067.10.262505
MA0068.10.0484013
MA0069.10.986045
MA0070.10.953942
MA0071.10.0216371
MA0072.10.0754622
MA0073.10.000383981
MA0074.12.73161
MA0076.10.0736437
MA0077.10.53984
MA0078.10.368331
MA0081.10.0589588
MA0083.10.0904428
MA0084.10.399926
MA0087.10.549804
MA0088.10.155969
MA0089.10
MA0090.10.590021
MA0091.17.42824
MA0092.11.24336
MA0093.14.74512e-05
MA0095.10
MA0098.10
MA0100.10.106898
MA0101.10.0241342
MA0103.10.995452
MA0105.19.36482e-06
MA0106.10.717674
MA0107.10.00470459
MA0108.22.30161
MA0109.10
MA0111.10.187943
MA0113.10.147657
MA0114.10.207303
MA0115.10.21275
MA0116.10.0291652
MA0117.10.10336
MA0119.10.556499
MA0122.10.368949
MA0124.11.04912
MA0125.10.434969
MA0130.10
MA0131.10.0826399
MA0132.10
MA0133.10
MA0135.15.19308
MA0136.10.00644613
MA0139.10.203169
MA0140.10.150096
MA0141.10.307918
MA0142.10.832321
MA0143.10.50965
MA0144.10.242946
MA0145.10.358329
MA0146.10.000717726
MA0147.10.00180267
MA0148.10.355821
MA0149.10.0188008
MA0062.26.06298e-05
MA0035.20.0208356
MA0039.20.00175829
MA0138.20.189642
MA0002.25.95795
MA0137.20.311752
MA0104.20.000931961
MA0047.20.675827
MA0112.20.076002
MA0065.20.19308
MA0150.10.564277
MA0151.10
MA0152.10.292096
MA0153.10.132299
MA0154.10.0178925
MA0155.10.458792
MA0156.10.033168
MA0157.10.0990362
MA0158.10
MA0159.10.983813
MA0160.10.59689
MA0161.10
MA0162.11.72135e-09
MA0163.10.0433248
MA0164.10.820982
MA0080.20.0227652
MA0018.20.00949654
MA0099.20.292823
MA0079.22.77938e-12
MA0102.20.429397
MA0258.10.0523365
MA0259.10.0175135
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
TAL1#688692.536014623556240.009387940804193650.0354240606130927



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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