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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 10:54, 17 September 2013


Full id: C199_glioblastoma_B_osteosarcoma_Fibroblast_heart_rhabdomyosarcoma_myxofibrosarcoma



Phase1 CAGE Peaks

Hg19::chr10:28030013..28030015,+p@chr10:28030013..28030015
+
Hg19::chr10:28033530..28033552,-p@chr10:28033530..28033552
-
Hg19::chr10:28033565..28033575,-p@chr10:28033565..28033575
-
Hg19::chr10:28033579..28033592,-p@chr10:28033579..28033592
-
Hg19::chr10:28033614..28033628,-p@chr10:28033614..28033628
-
Hg19::chr10:28033640..28033643,-p@chr10:28033640..28033643
-
Hg19::chr10:28033659..28033673,+p3@ENST00000419777
Hg19::chr10:28033753..28033766,+p4@ENST00000419777
Hg19::chr10:28033776..28033788,+p1@ENST00000419777
Hg19::chr10:28033806..28033813,+p5@ENST00000419777
Hg19::chr10:28033817..28033825,+p2@ENST00000419777
Hg19::chr10:28034395..28034404,-p9@MKX
Hg19::chr10:28034450..28034462,+p@chr10:28034450..28034462
+
Hg19::chr10:28035746..28035751,-p@chr10:28035746..28035751
-
Hg19::chr10:28287942..28287952,-p8@ARMC4
Hg19::chr10:28287968..28288010,-p1@ARMC4
Hg19::chr10:28367310..28367318,+p@chr10:28367310..28367318
+
Hg19::chr10:28414812..28414824,-p@chr10:28414812..28414824
-
Hg19::chr10:28488010..28488022,-p@chr10:28488010..28488022
-
Hg19::chr10:28491892..28491902,-p7@MPP7
Hg19::chr10:28506871..28506903,-p@chr10:28506871..28506903
-
Hg19::chr10:28506967..28506974,-p@chr10:28506967..28506974
-
Hg19::chr10:28507002..28507009,-p@chr10:28507002..28507009
-
Hg19::chr10:28509539..28509568,-p@chr10:28509539..28509568
-
Hg19::chr10:28509632..28509637,-p@chr10:28509632..28509637
-
Hg19::chr10:28509658..28509676,-p@chr10:28509658..28509676
-
Hg19::chr10:28509721..28509724,-p@chr10:28509721..28509724
-
Hg19::chr10:28527477..28527523,+p@chr10:28527477..28527523
+
Hg19::chr10:28527860..28527872,-p9@MPP7
Hg19::chr10:28530804..28530813,-p@chr10:28530804..28530813
-
Hg19::chr10:28530831..28530841,-p@chr10:28530831..28530841
-
Hg19::chr10:54329319..54329326,-p@chr10:54329319..54329326
-
Hg19::chr10:54329365..54329373,-p@chr10:54329365..54329373
-
Hg19::chr10:54329394..54329397,-p@chr10:54329394..54329397
-
Hg19::chr10:54329422..54329434,-p@chr10:54329422..54329434
-
Hg19::chr10:54329447..54329454,-p@chr10:54329447..54329454
-
Hg19::chr10:54373438..54373447,-p@chr10:54373438..54373447
-
Hg19::chr10:54399928..54399940,+p@chr10:54399928..54399940
+
Hg19::chr10:54399943..54399963,+p@chr10:54399943..54399963
+
Hg19::chr15:36045989..36046028,+p@chr15:36045989..36046028
+
Hg19::chr18:38446239..38446249,-p@chr18:38446239..38446249
-
Hg19::chr18:38529517..38529528,+p@chr18:38529517..38529528
+
Hg19::chr18:38529571..38529575,+p@chr18:38529571..38529575
+
Hg19::chr18:39041105..39041117,-p@chr18:39041105..39041117
-
Hg19::chr18:70417486..70417495,-p@chr18:70417486..70417495
-
Hg19::chr18:70417532..70417548,-p@chr18:70417532..70417548
-
Hg19::chr18:70417551..70417561,-p@chr18:70417551..70417561
-
Hg19::chr18:70417646..70417651,-p@chr18:70417646..70417651
-
Hg19::chr18:70417659..70417666,-p@chr18:70417659..70417666
-
Hg19::chr18:70423377..70423388,-p@chr18:70423377..70423388
-
Hg19::chr1:170043617..170043675,-p2@KIFAP3
Hg19::chr1:170043681..170043695,-p3@KIFAP3
Hg19::chr1:170043917..170043928,-p4@KIFAP3
Hg19::chr1:198636194..198636203,-p4@ENST00000413577
Hg19::chr1:70541774..70541784,+p@chr1:70541774..70541784
+
Hg19::chr21:26714477..26714509,+p@chr21:26714477..26714509
+
Hg19::chr21:26714551..26714589,+p@chr21:26714551..26714589
+
Hg19::chr2:70025987..70025999,-p5@ENST00000502349
p5@uc002sft.1
Hg19::chr2:70026040..70026056,-p4@ENST00000502349
p4@uc002sft.1
Hg19::chr2:70026073..70026084,-p3@ENST00000502349
p3@uc002sft.1
Hg19::chr3:30166734..30166774,+p@chr3:30166734..30166774
+
Hg19::chr3:30274017..30274027,-p@chr3:30274017..30274027
-
Hg19::chr3:30274089..30274100,-p@chr3:30274089..30274100
-
Hg19::chr4:176708533..176708544,-p28@GPM6A
Hg19::chr4:176729849..176729872,+p@chr4:176729849..176729872
+
Hg19::chr4:176734130..176734137,-p33@GPM6A
Hg19::chr4:176749234..176749238,+p@chr4:176749234..176749238
+
Hg19::chr4:176749383..176749408,+p@chr4:176749383..176749408
+
Hg19::chr5:103227130..103227137,-p@chr5:103227130..103227137
-
Hg19::chr5:103227146..103227159,-p@chr5:103227146..103227159
-
Hg19::chr5:103248950..103248994,+p@chr5:103248950..103248994
+
Hg19::chr5:103251049..103251059,+p@chr5:103251049..103251059
+
Hg19::chr5:169014305..169014309,+p8@CCDC99
Hg19::chr5:169122140..169122157,+p3@DOCK2
Hg19::chr5:169122159..169122169,+p5@DOCK2
Hg19::chr5:24160807..24160831,-p@chr5:24160807..24160831
-
Hg19::chr5:24163239..24163250,-p@chr5:24163239..24163250
-
Hg19::chr5:24170343..24170359,+p3@ENST00000514047
Hg19::chr6:113010123..113010128,-p@chr6:113010123..113010128
-
Hg19::chr6:73270707..73270718,-p@chr6:73270707..73270718
-
Hg19::chr9:106443940..106443941,+p@chr9:106443940..106443941
+
Hg19::chrY:18192344..18192349,+p@chrY:18192344..18192349
+
Hg19::chrY:3781821..3781829,-p@chrY:3781821..3781829
-


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:0016939kinesin II complex0.019604380077711
GO:0042608T cell receptor binding0.0261334029735661
GO:0048247lymphocyte chemotaxis0.0261334029735661
GO:0030676Rac guanyl-nucleotide exchange factor activity0.0342925194531488
GO:0019894kinesin binding0.03526711454817



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>

Uber Anatomy
Ontology termp-valuen
brain6.59e-0768
future brain6.59e-0768
Disease
Ontology termp-valuen
nervous system cancer5.98e-3411


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)
MA0003.11.06031e-11
MA0004.10.0844656
MA0006.13.72593
MA0007.10.0227937
MA0009.10.414682
MA0014.11.67433e-11
MA0017.10.117734
MA0019.10.242039
MA0024.10.0847075
MA0025.10.601391
MA0027.11.52208
MA0028.10.000457959
MA0029.10.309245
MA0030.11.53162
MA0031.11.28072
MA0038.10.602859
MA0040.10.0952719
MA0041.11.1739
MA0042.12.50929
MA0043.10.415094
MA0046.10.798122
MA0048.10.0675703
MA0050.10.494655
MA0051.10.590537
MA0052.10.320587
MA0055.10.000393417
MA0056.10
MA0057.11.424e-05
MA0058.10.0297386
MA0059.10.0292348
MA0060.10.0407311
MA0061.10.0215883
MA0063.10
MA0066.10.0153188
MA0067.11.60152
MA0068.14.7803e-05
MA0069.11.86718
MA0070.10.381375
MA0071.10.754799
MA0072.10.755449
MA0073.10.335548
MA0074.10.0682916
MA0076.10.0104267
MA0077.10.114094
MA0078.10.133491
MA0081.10.608647
MA0083.10.424525
MA0084.11.2153
MA0087.10.750161
MA0088.10.00294227
MA0089.10
MA0090.10.525963
MA0091.10.188886
MA0092.10.893546
MA0093.10.0336844
MA0095.10
MA0098.10
MA0100.10.0173095
MA0101.10.150001
MA0103.10.0641772
MA0105.10.000373018
MA0106.10.0954036
MA0107.10.100518
MA0108.20.838076
MA0109.10
MA0111.13.48074
MA0113.10.106298
MA0114.10.158291
MA0115.10.767535
MA0116.10.550169
MA0117.10.1528
MA0119.10.229
MA0122.10.167232
MA0124.10.702054
MA0125.10.197947
MA0130.10
MA0131.10.147936
MA0132.10
MA0133.10
MA0135.10.890537
MA0136.10.376529
MA0139.10.0023659
MA0140.10.745019
MA0141.10.411504
MA0142.10.759389
MA0143.11.55363
MA0144.10.128306
MA0145.10.0026773
MA0146.11.31815e-11
MA0147.10.414513
MA0148.11.20875
MA0149.10.00914493
MA0062.20.000892037
MA0035.21.05213
MA0039.20.000248903
MA0138.20.0333101
MA0002.20.349287
MA0137.20.444493
MA0104.20.541492
MA0047.21.83807
MA0112.23.19438e-07
MA0065.20.0121461
MA0150.10.328167
MA0151.10
MA0152.10.769263
MA0153.10.550492
MA0154.10.000915089
MA0155.16.66961e-05
MA0156.10.860994
MA0157.12.0055
MA0158.10
MA0159.10.0606191
MA0160.10.431449
MA0161.10
MA0162.10.00776855
MA0163.10.00014296
MA0164.10.114987
MA0080.20.538476
MA0018.20.0221366
MA0099.20.0537463
MA0079.20
MA0102.20.515212
MA0258.10.00124872
MA0259.10.125767
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
CTBP2#148896.800638591011487.49081057670852e-060.000214455253788613
SETDB1#986973.400484135494860.004624451112347620.0218401487619822
SIRT6#5154847.404260433254210.002183284878690650.0125929248050794
SUZ12#23512127.245655071478971.02249555920046e-075.98925483496003e-06



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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