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

Latest revision as of 10:44, 17 September 2013


Full id: C153_rhabdomyosarcoma_liposarcoma_pancreatic_somatostatinoma_Reticulocytes_lymphoma_testicular



Phase1 CAGE Peaks

Hg19::chr10:130726859..130726861,-p@chr10:130726859..130726861
-
Hg19::chr11:22688150..22688192,+p2@GAS2
Hg19::chr11:22688234..22688267,+p6@GAS2
Hg19::chr11:61310346..61310389,-p1@uc001nrw.1
Hg19::chr12:3309487..3309524,+p@chr12:3309487..3309524
+
Hg19::chr12:6069998..6070025,-p@chr12:6069998..6070025
-
Hg19::chr12:68519344..68519345,+p@chr12:68519344..68519345
+
Hg19::chr12:68542919..68542955,+p@chr12:68542919..68542955
+
Hg19::chr12:68567714..68567717,+p@chr12:68567714..68567717
+
Hg19::chr12:68570993..68570996,+p@chr12:68570993..68570996
+
Hg19::chr12:68617683..68617703,+p@chr12:68617683..68617703
+
Hg19::chr12:68696657..68696661,-p4@MDM1
Hg19::chr12:68726052..68726117,-p1@MDM1
Hg19::chr12:68726131..68726159,-p2@MDM1
Hg19::chr12:69080734..69080808,+p1@NUP107
Hg19::chr12:69106435..69106441,+p@chr12:69106435..69106441
+
Hg19::chr12:69201923..69202028,+p1@MDM2
Hg19::chr12:69234561..69234599,+p@chr12:69234561..69234599
+
Hg19::chr12:69367558..69367560,+p@chr12:69367558..69367560
+
Hg19::chr12:69418868..69418872,+p@chr12:69418868..69418872
+
Hg19::chr12:69594803..69594810,-p@chr12:69594803..69594810
-
Hg19::chr12:69609220..69609225,-p@chr12:69609220..69609225
-
Hg19::chr12:69621970..69621975,-p@chr12:69621970..69621975
-
Hg19::chr12:69633341..69633366,+p1@CPSF6
Hg19::chr12:69633372..69633390,+p2@CPSF6
Hg19::chr12:69633407..69633421,+p3@CPSF6
Hg19::chr12:69641162..69641166,+p@chr12:69641162..69641166
+
Hg19::chr12:69652342..69652353,+p17@CPSF6
Hg19::chr12:69653866..69653876,+p@chr12:69653866..69653876
+
Hg19::chr12:69659244..69659255,+p@chr12:69659244..69659255
+
Hg19::chr12:69659283..69659302,+p@chr12:69659283..69659302
+
Hg19::chr12:69659340..69659357,+p@chr12:69659340..69659357
+
Hg19::chr12:69662136..69662137,+p4@AK093765
Hg19::chr12:69665761..69665770,+p31@CPSF6
Hg19::chr12:69665801..69665808,+p55@CPSF6
Hg19::chr12:69665946..69665955,+p7@CPSF6
Hg19::chr12:69667727..69667732,+p@chr12:69667727..69667732
+
Hg19::chr12:69667739..69667749,+p@chr12:69667739..69667749
+
Hg19::chr12:69667813..69667827,+p@chr12:69667813..69667827
+
Hg19::chr12:69667906..69667909,+p@chr12:69667906..69667909
+
Hg19::chr12:69676194..69676198,+p@chr12:69676194..69676198
+
Hg19::chr12:69678255..69678259,+p1@ENST00000548895
Hg19::chr12:69753448..69753577,+p1@YEATS4
Hg19::chr12:69754026..69754035,+p@chr12:69754026..69754035
+
Hg19::chr12:69754055..69754064,+p@chr12:69754055..69754064
+
Hg19::chr12:69841002..69841005,+p@chr12:69841002..69841005
+
Hg19::chr12:69864058..69864077,-p@chr12:69864058..69864077
-
Hg19::chr12:69864149..69864222,+p1@FRS2
Hg19::chr12:69875077..69875081,+p@chr12:69875077..69875081
+
Hg19::chr12:69879976..69879979,+p@chr12:69879976..69879979
+
Hg19::chr12:69885308..69885312,+p@chr12:69885308..69885312
+
Hg19::chr12:69909563..69909567,+p@chr12:69909563..69909567
+
Hg19::chr12:69914174..69914177,+p@chr12:69914174..69914177
+
Hg19::chr12:69921143..69921147,+p@chr12:69921143..69921147
+
Hg19::chr12:69937876..69937902,+p@chr12:69937876..69937902
+
Hg19::chr12:69975438..69975442,+p@chr12:69975438..69975442
+
Hg19::chr12:69979084..69979095,-p1@MIR3913-1
Hg19::chr12:69979210..69979252,+p1@CCT2
Hg19::chr12:69979270..69979281,+p2@CCT2
Hg19::chr12:69979638..69979683,+p3@CCT2
Hg19::chr12:69980043..69980088,+p4@CCT2
Hg19::chr12:69980539..69980551,+p@chr12:69980539..69980551
+
Hg19::chr12:69981346..69981356,+p@chr12:69981346..69981356
+
Hg19::chr12:69981711..69981716,+p@chr12:69981711..69981716
+
Hg19::chr12:69981962..69982010,+p@chr12:69981962..69982010
+
Hg19::chr12:69983331..69983347,+p8@CCT2
Hg19::chr12:69987281..69987295,+p@chr12:69987281..69987295
+
Hg19::chr12:69987298..69987312,+p@chr12:69987298..69987312
+
Hg19::chr12:69996323..69996329,+p@chr12:69996323..69996329
+
Hg19::chr12:69996460..69996463,+p@chr12:69996460..69996463
+
Hg19::chr12:70000134..70000135,-p@chr12:70000134..70000135
-
Hg19::chr12:70008447..70008458,+p@chr12:70008447..70008458
+
Hg19::chr12:70013307..70013310,+p@chr12:70013307..70013310
+
Hg19::chr12:70383686..70383688,+p@chr12:70383686..70383688
+
Hg19::chr12:70389117..70389122,+p@chr12:70389117..70389122
+
Hg19::chr12:70389143..70389146,+p@chr12:70389143..70389146
+
Hg19::chr12:70391649..70391654,+p@chr12:70391649..70391654
+
Hg19::chr12:78224657..78224661,+p42@NAV3
Hg19::chr12:78224667..78224680,+p5@NAV3
Hg19::chr12:80980430..80980454,+p@chr12:80980430..80980454
+
Hg19::chr13:31437561..31437585,+p@chr13:31437561..31437585
+
Hg19::chr16:7137754..7137799,+p@chr16:7137754..7137799
+
Hg19::chr19:50993024..50993039,-p@chr19:50993024..50993039
-
Hg19::chr1:188791348..188791353,-p@chr1:188791348..188791353
-
Hg19::chr1:188791367..188791376,-p@chr1:188791367..188791376
-
Hg19::chr22:46420766..46420774,+p@chr22:46420766..46420774
+
Hg19::chr2:144238354..144238358,-p1@ENST00000549032
p1@ENST00000550516
Hg19::chr2:144291788..144291791,+p@chr2:144291788..144291791
+
Hg19::chr2:144551351..144551352,-p@chr2:144551351..144551352
-
Hg19::chr2:144661193..144661223,-p@chr2:144661193..144661223
-
Hg19::chr2:155831065..155831074,+p@chr2:155831065..155831074
+
Hg19::chr2:156009264..156009270,-p@chr2:156009264..156009270
-
Hg19::chr2:190927424..190927436,-p2@MSTN
Hg19::chr2:190927447..190927466,-p1@MSTN
Hg19::chr3:106909444..106909465,-p@chr3:106909444..106909465
-
Hg19::chr3:587825..587862,+p@chr3:587825..587862
+
Hg19::chr3:587869..587880,+p@chr3:587869..587880
+
Hg19::chr4:138289924..138289941,-p@chr4:138289924..138289941
-
Hg19::chr4:138290008..138290015,-p@chr4:138290008..138290015
-
Hg19::chr5:103638280..103638288,+p@chr5:103638280..103638288
+
Hg19::chr5:73209060..73209067,-p@chr5:73209060..73209067
-
Hg19::chr6:113168012..113168027,-p@chr6:113168012..113168027
-
Hg19::chr6:113433185..113433188,-p@chr6:113433185..113433188
-
Hg19::chr6:23609145..23609162,-p@chr6:23609145..23609162
-
Hg19::chr7:150864780..150864785,-p1@GBX1
Hg19::chr7:84816235..84816246,-p7@SEMA3D
Hg19::chr7:84816288..84816301,-p3@SEMA3D
Hg19::chr7:84816323..84816334,-p6@SEMA3D
Hg19::chr7:84816338..84816354,-p5@SEMA3D
Hg19::chr7:84816355..84816384,-p2@SEMA3D
Hg19::chr7:85221253..85221277,+p@chr7:85221253..85221277
+
Hg19::chr9:9967081..9967122,-p@chr9:9967081..9967122
-


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:0044428nuclear part0.000291093060930528
GO:0044446intracellular organelle part0.0185156016870656
GO:0044422organelle part0.0185156016870656
GO:0046619optic placode formation involved in camera-type eye0.0208052367719173
GO:0001743optic placode formation0.0208052367719173
GO:0048856anatomical structure development0.0208052367719173
GO:0044453nuclear membrane part0.0221793827284334
GO:0005654nucleoplasm0.0221793827284334
GO:0042382paraspeckles0.0221793827284334
GO:0017163negative regulator of basal transcription activity0.0221793827284334
GO:0005069transmembrane receptor protein tyrosine kinase docking protein activity0.0277017948375343
GO:0005849mRNA cleavage factor complex0.0277017948375343
GO:0031965nuclear membrane0.0277017948375343
GO:0005832chaperonin-containing T-complex0.0277017948375343
GO:0031981nuclear lumen0.0277017948375343
GO:0005068transmembrane receptor protein tyrosine kinase adaptor protein activity0.0277017948375343
GO:0044424intracellular part0.0277017948375343
GO:0005634nucleus0.0277017948375343
GO:0005635nuclear envelope0.0277017948375343
GO:0007185transmembrane receptor protein tyrosine phosphatase signaling pathway0.0277017948375343
GO:0016299regulator of G-protein signaling activity0.0277017948375343
GO:0007350blastoderm segmentation0.0277017948375343
GO:0010092specification of organ identity0.0277017948375343
GO:0000578embryonic axis specification0.0277017948375343
GO:0005487nucleocytoplasmic transporter activity0.0277017948375343
GO:0008595determination of anterior/posterior axis, embryo0.0277017948375343
GO:0001759induction of an organ0.0277017948375343
GO:0007351tripartite regional subdivision0.0277017948375343
GO:0031128induction0.0295437981484139
GO:0045168cell-cell signaling during cell fate commitment0.0295437981484139
GO:0005066transmembrane receptor protein tyrosine kinase signaling protein activity0.0321594126627902
GO:0009948anterior/posterior axis specification0.0348827170122456
GO:0019211phosphatase activator activity0.0348827170122456
GO:0005640nuclear outer membrane0.0348827170122456
GO:0032502developmental process0.0348827170122456
GO:0045941positive regulation of transcription0.0348827170122456
GO:0043233organelle lumen0.0348827170122456
GO:0031974membrane-enclosed lumen0.0348827170122456
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0359773746716329
GO:0048593camera-type eye morphogenesis0.0359773746716329
GO:0007167enzyme linked receptor protein signaling pathway0.0370562632147988
GO:0009653anatomical structure morphogenesis0.0389763123615684
GO:0008543fibroblast growth factor receptor signaling pathway0.0411705597649131
GO:0007405neuroblast proliferation0.0417927904532598
GO:0042176regulation of protein catabolic process0.0417927904532598
GO:0009798axis specification0.0432822027145743
GO:0005626insoluble fraction0.0462882495288097
GO:0031325positive regulation of cellular metabolic process0.0462882495288097
GO:0006406mRNA export from nucleus0.0496295325094347
GO:0009893positive regulation of metabolic process0.0498426328458537
GO:0005158insulin receptor binding0.0498426328458537



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><br><br>disease_data<br>

Disease
Ontology termp-valuen
sarcoma2.29e-1120


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)
MA0003.13.93355e-09
MA0004.10.0696338
MA0006.10.00150043
MA0007.10.118722
MA0009.10.0785602
MA0014.14.85378e-06
MA0017.10.0313753
MA0019.10.946281
MA0024.10.68231
MA0025.10.846013
MA0027.11.39425
MA0028.10.238934
MA0029.10.415796
MA0030.10.702212
MA0031.11.24931
MA0038.10.516699
MA0040.11.14467
MA0041.12.21146
MA0042.10.984242
MA0043.10.270486
MA0046.10.074459
MA0048.10.0631489
MA0050.10.226135
MA0051.11.02423
MA0052.12.15666
MA0055.11.09656
MA0056.10
MA0057.10.00343036
MA0058.10.0463384
MA0059.10.000145157
MA0060.10.067818
MA0061.10.00936742
MA0063.10
MA0066.10.08064
MA0067.10.247007
MA0068.12.77737
MA0069.10.542084
MA0070.10.243078
MA0071.10.0171949
MA0072.10.512882
MA0073.10
MA0074.10.0768725
MA0076.10.833735
MA0077.10.857704
MA0078.10.553127
MA0081.10.734934
MA0083.10.58457
MA0084.10.993629
MA0087.11.31536
MA0088.10.00169041
MA0089.10
MA0090.10.134335
MA0091.11.37458
MA0092.10.183277
MA0093.10.0371926
MA0095.10
MA0098.10
MA0100.10.0905031
MA0101.10.133554
MA0103.10.0598059
MA0105.13.41973e-06
MA0106.10.0394734
MA0107.10.0187305
MA0108.20.538441
MA0109.10
MA0111.10.259537
MA0113.10.0456672
MA0114.10.0618608
MA0115.10.198631
MA0116.10.0203249
MA0117.10.311674
MA0119.10.645649
MA0122.10.341771
MA0124.10.51772
MA0125.10.806876
MA0130.10
MA0131.10.362664
MA0132.10
MA0133.10
MA0135.10.303477
MA0136.10.186891
MA0139.10.151247
MA0140.10.240762
MA0141.10.0182186
MA0142.11.11719
MA0143.12.16897
MA0144.10.126434
MA0145.11.87188e-07
MA0146.10.000197257
MA0147.10.00110845
MA0148.10.476514
MA0149.10.00234635
MA0062.20.325829
MA0035.20.12601
MA0039.21.50598e-07
MA0138.20.0130956
MA0002.20.00724908
MA0137.20.375532
MA0104.20.00166175
MA0047.20.877737
MA0112.22.92385e-09
MA0065.20.0327493
MA0150.10.0648423
MA0151.10
MA0152.10.416683
MA0153.10.384495
MA0154.10.000631402
MA0155.10.000774639
MA0156.10.264
MA0157.11.00744
MA0158.10
MA0159.10.000260554
MA0160.10.20388
MA0161.10
MA0162.13.38679e-07
MA0163.17.08294e-05
MA0164.10.284358
MA0080.20.037249
MA0018.20.239296
MA0099.20.0180789
MA0079.26.39899e-12
MA0102.20.410749
MA0258.10.00118787
MA0259.10.0119828
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
GTF2B#2959102.852127672707520.002798251988128870.0153209247385683



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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