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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:03, 17 September 2013


Full id: C237_acute_breast_testicular_hepatoblastoma_chronic_argyrophil_Bronchial



Phase1 CAGE Peaks

Hg19::chr10:103875750..103875763,-p@chr10:103875750..103875763
-
Hg19::chr10:98561308..98561327,+p@chr10:98561308..98561327
+
Hg19::chr11:62623024..62623031,-p10@SNHG1
Hg19::chr11:64412661..64412665,-p@chr11:64412661..64412665
-
Hg19::chr12:11891065..11891095,+p@chr12:11891065..11891095
+
Hg19::chr14:104398010..104398021,+p@chr14:104398010..104398021
+
Hg19::chr14:77640277..77640278,+p@chr14:77640277..77640278
+
Hg19::chr15:34729927..34729938,-p3@GOLGA8A
Hg19::chr15:34729970..34730066,-p1@GOLGA8A
Hg19::chr15:34730068..34730078,-p4@GOLGA8A
Hg19::chr15:50242782..50242788,-p@chr15:50242782..50242788
-
Hg19::chr16:20698317..20698321,+p@chr16:20698317..20698321
+
Hg19::chr16:54097622..54097627,+p4@FTO
Hg19::chr16:85605565..85605633,+p@chr16:85605565..85605633
+
Hg19::chr16:85605833..85605846,+p@chr16:85605833..85605846
+
Hg19::chr19:16177826..16177832,+p13@TPM4
Hg19::chr19:20228118..20228148,+p@chr19:20228118..20228148
+
Hg19::chr19:23507187..23507221,-p@chr19:23507187..23507221
-
Hg19::chr19:5977239..5977241,+p@chr19:5977239..5977241
+
Hg19::chr19:807513..807524,+p@chr19:807513..807524
+
Hg19::chr1:157244660..157244683,+p@chr1:157244660..157244683
+
Hg19::chr1:45187567..45187581,-p1@RNU5F-1
Hg19::chr1:67217919..67217946,+p3@TCTEX1D1
Hg19::chr1:67217948..67217959,+p8@TCTEX1D1
Hg19::chr1:67217960..67217971,+p6@TCTEX1D1
Hg19::chr1:67218038..67218049,+p7@TCTEX1D1
Hg19::chr1:67218064..67218079,+p4@TCTEX1D1
Hg19::chr20:2781462..2781481,-p3@CPXM1
Hg19::chr21:38788638..38788642,+p@chr21:38788638..38788642
+
Hg19::chr21:44260635..44260732,-p@chr21:44260635..44260732
-
Hg19::chr21:46572430..46572455,+p3@ADARB1
Hg19::chr2:158005569..158005571,-p@chr2:158005569..158005571
-
Hg19::chr2:27659844..27659848,+p@chr2:27659844..27659848
+
Hg19::chr2:43233377..43233385,-p1@ENST00000457457
Hg19::chr3:129089204..129089226,-p@chr3:129089204..129089226
-
Hg19::chr3:155273028..155273031,-p5@AK093601
Hg19::chr3:159944665..159944676,-p@chr3:159944665..159944676
-
Hg19::chr3:185912589..185912593,-p@chr3:185912589..185912593
-
Hg19::chr3:6573724..6573727,+p@chr3:6573724..6573727
+
Hg19::chr4:112390198..112390199,-p@chr4:112390198..112390199
-
Hg19::chr4:130454725..130454734,+p@chr4:130454725..130454734
+
Hg19::chr4:130454750..130454759,+p@chr4:130454750..130454759
+
Hg19::chr5:10589332..10589341,+p@chr5:10589332..10589341
+
Hg19::chr5:7891424..7891428,+p3@MTRR
Hg19::chr5:79948119..79948125,+p@chr5:79948119..79948125
+
Hg19::chr6:135504165..135504169,+p@chr6:135504165..135504169
+
Hg19::chr7:158456920..158456961,-p@chr7:158456920..158456961
-
Hg19::chr8:101725067..101725135,-p18@PABPC1
Hg19::chr8:129015089..129015108,+p@chr8:129015089..129015108
+
Hg19::chr8:25138504..25138508,+p@chr8:25138504..25138508
+
Hg19::chr8:74495107..74495112,-p14@STAU2
Hg19::chr9:133729353..133729355,+p1@M14755
Hg19::chr9:19464599..19464604,-p1@ENST00000438342
Hg19::chrX:113152537..113152540,-p@chrX:113152537..113152540
-
Hg19::chrX:125607014..125607031,+p3@MTND4P24
Hg19::chrX:153169072..153169090,-p@chrX:153169072..153169090
-
Hg19::chrX:62060354..62060357,+p@chrX:62060354..62060357
+
Hg19::chrY:10037829..10037843,+p@chrY:10037829..10037843
+


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:0003725double-stranded RNA binding0.0152813587546557
GO:0050429calcium-dependent phospholipase C activity0.0158071352878841
GO:0030586[methionine synthase] reductase activity0.0158071352878841
GO:0002102podosome0.0237023284550814
GO:0043489RNA stabilization0.0237023284550814
GO:0048255mRNA stabilization0.0237023284550814
GO:0005862muscle thin filament tropomyosin0.0237023284550814
GO:0016723oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor0.0237023284550814
GO:0008494translation activator activity0.0263328196997464
GO:0003723RNA binding0.0266309397753402
GO:0016722oxidoreductase activity, oxidizing metal ions0.0266309397753402
GO:0008143poly(A) binding0.0266309397753402
GO:0043487regulation of RNA stability0.0266309397753402
GO:0043488regulation of mRNA stability0.0266309397753402
GO:0006397mRNA processing0.0266309397753402
GO:0006378mRNA polyadenylation0.0266494259946061
GO:0031941filamentous actin0.0278653998270325
GO:0005865striated muscle thin filament0.0286760276701247
GO:0043631RNA polyadenylation0.0286760276701247
GO:0009086methionine biosynthetic process0.0286760276701247
GO:0016071mRNA metabolic process0.0286760276701247
GO:0031124mRNA 3'-end processing0.0286760276701247
GO:0004000adenosine deaminase activity0.0286760276701247
GO:0009067aspartate family amino acid biosynthetic process0.0286760276701247
GO:0007368determination of left/right symmetry0.0286760276701247
GO:0009799determination of symmetry0.0286760276701247
GO:0006555methionine metabolic process0.0286760276701247
GO:0009855determination of bilateral symmetry0.0286760276701247
GO:0031123RNA 3'-end processing0.0286760276701247
GO:0051252regulation of RNA metabolic process0.0286760276701247
GO:0005737cytoplasm0.0286760276701247
GO:0000097sulfur amino acid biosynthetic process0.0286760276701247
GO:0003727single-stranded RNA binding0.0286760276701247
GO:0030863cortical cytoskeleton0.0337768623811976
GO:0005884actin filament0.0337768623811976
GO:0009066aspartate family amino acid metabolic process0.0366529326244527
GO:0000096sulfur amino acid metabolic process0.0366529326244527
GO:0010181FMN binding0.0366529326244527
GO:0006396RNA processing0.0366529326244527
GO:0030326embryonic limb morphogenesis0.037173879012475
GO:0035113embryonic appendage morphogenesis0.037173879012475
GO:0003729mRNA binding0.037173879012475
GO:0060173limb development0.037173879012475
GO:0035107appendage morphogenesis0.037173879012475
GO:0035108limb morphogenesis0.037173879012475
GO:0050661NADP binding0.037173879012475
GO:0048736appendage development0.037173879012475
GO:0008307structural constituent of muscle0.0393137042532833
GO:0004182carboxypeptidase A activity0.0393137042532833
GO:0019239deaminase activity0.0393137042532833
GO:0004435phosphoinositide phospholipase C activity0.0393137042532833
GO:0044448cell cortex part0.0393137042532833
GO:0004434inositol or phosphatidylinositol phosphodiesterase activity0.0393137042532833
GO:0044272sulfur compound biosynthetic process0.0393137042532833
GO:0030017sarcomere0.0405361090424083
GO:0016814hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines0.0405361090424083
GO:0004181metallocarboxypeptidase activity0.0405361090424083
GO:0030016myofibril0.0430689565710222
GO:0004629phospholipase C activity0.0455129486911617
GO:0044449contractile fiber part0.047093273688738
GO:0005938cell cortex0.0485895469257875
GO:0043292contractile fiber0.0485895469257875



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><br>disease_data<br>

Disease
Ontology termp-valuen
myeloid leukemia6.80e-5731
leukemia3.03e-4539
hematologic cancer1.31e-3451
immune system cancer1.31e-3451
chronic myeloid leukemia5.13e-231
organ system cancer1.04e-12137
chronic leukemia4.94e-128
cancer2.69e-07235
disease of cellular proliferation3.89e-07239


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)
MA0003.18.14184e-06
MA0004.10.419347
MA0006.10.24686
MA0007.10.0752445
MA0009.10.621427
MA0014.10.000661716
MA0017.10.186708
MA0019.10.210287
MA0024.10.911787
MA0025.10.834774
MA0027.11.67575
MA0028.10.0214147
MA0029.10.494881
MA0030.10.478645
MA0031.10.123603
MA0038.10.0434269
MA0040.10.168336
MA0041.11.09423
MA0042.12.20415
MA0043.10.621911
MA0046.10.210453
MA0048.10.00392665
MA0050.10.0173802
MA0051.10.163028
MA0052.10.980702
MA0055.10.00217488
MA0056.10
MA0057.10.488537
MA0058.10.00705038
MA0059.10.106593
MA0060.10.00202577
MA0061.10.00469439
MA0063.10
MA0066.11.04748
MA0067.10.454522
MA0068.10.427181
MA0069.10.598958
MA0070.11.10196
MA0071.11.30007
MA0072.11.09087
MA0073.119.853
MA0074.10.0419937
MA0076.10.123514
MA0077.10.563808
MA0078.11.95487
MA0081.10.106747
MA0083.10.222368
MA0084.10.615132
MA0087.10.196553
MA0088.10.0057715
MA0089.10
MA0090.11.81511
MA0091.10.0885368
MA0092.10.173301
MA0093.10.253397
MA0095.10
MA0098.10
MA0100.10.17969
MA0101.10.260582
MA0103.10.05035
MA0105.10.00542693
MA0106.10.0564023
MA0107.10.123818
MA0108.21.83828
MA0109.10
MA0111.10.309835
MA0113.10.48475
MA0114.10.210103
MA0115.10.392652
MA0116.11.00165
MA0117.10.242391
MA0119.10.199194
MA0122.10.260132
MA0124.10.94614
MA0125.10.805219
MA0130.10
MA0131.10.284188
MA0132.10
MA0133.10
MA0135.10.66845
MA0136.10.694143
MA0139.10.979874
MA0140.10.566465
MA0141.10.104955
MA0142.10.107962
MA0143.10.223349
MA0144.10.178459
MA0145.10.0624862
MA0146.10.00010684
MA0147.10.134537
MA0148.10.103741
MA0149.12.17444
MA0062.20.0134134
MA0035.20.564674
MA0039.27.74332e-11
MA0138.20.560638
MA0002.20.279901
MA0137.20.072043
MA0104.20.0603348
MA0047.20.0523797
MA0112.20.0508868
MA0065.20.161706
MA0150.10.132442
MA0151.10
MA0152.10.583243
MA0153.10.284938
MA0154.10.0813983
MA0155.10.0232069
MA0156.10.488321
MA0157.10.31617
MA0158.10
MA0159.10.025226
MA0160.10.51385
MA0161.10
MA0162.16.19255e-06
MA0163.10.029356
MA0164.10.872807
MA0080.20.626481
MA0018.20.0568715
MA0099.20.0340801
MA0079.20
MA0102.20.64826
MA0258.10.782021
MA0259.11.38259
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
BRF2#55290237.05433039294310.001375248246011580.00896060587467734
GATA2#2624132.856622629934520.0004632234259209770.00426543743429386
KAT2A#2648221.24448275862070.004087663871803450.0195186323659144
SIRT6#51548513.24468999914013.988468326839e-050.000742913578717207
XRCC4#7518174.10866078588610.01340667023203250.0473705674390432



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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