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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.280667563736426

Latest revision as of 11:00, 17 September 2013


Full id: C223_Chondrocyte_basal_renal_Fibroblast_Smooth_spindle_Synoviocyte



Phase1 CAGE Peaks

Hg19::chr16:16235190..16235222,+p3@ABCC1
Hg19::chr16:367222..367228,+p@chr16:367222..367228
+
Hg19::chr16:66906996..66906997,-p@chr16:66906996..66906997
-
Hg19::chr1:203148096..203148127,-p@chr1:203148096..203148127
-
Hg19::chr7:150824026..150824027,-p@chr7:150824026..150824027
-
Hg19::chr7:45951982..45952024,-p@chr7:45951982..45952024
-
Hg19::chr7:45952071..45952083,-p@chr7:45952071..45952083
-
Hg19::chr7:45952219..45952234,+p@chr7:45952219..45952234
+
Hg19::chr7:45952362..45952373,-p25@IGFBP3
Hg19::chr7:45952409..45952422,+p@chr7:45952409..45952422
+
Hg19::chr7:45952418..45952432,-p11@IGFBP3
Hg19::chr7:45952439..45952454,-p10@IGFBP3
Hg19::chr7:45952448..45952473,+p@chr7:45952448..45952473
+
Hg19::chr7:45952458..45952470,-p12@IGFBP3
Hg19::chr7:45952526..45952533,-p32@IGFBP3
Hg19::chr7:45952542..45952547,-p31@IGFBP3
Hg19::chr7:45952555..45952566,-p18@IGFBP3
Hg19::chr7:45952575..45952582,-p26@IGFBP3
Hg19::chr7:45952609..45952694,+p@chr7:45952609..45952694
+
Hg19::chr7:45952626..45952637,-p23@IGFBP3
Hg19::chr7:45952643..45952654,-p22@IGFBP3
Hg19::chr7:45952665..45952679,-p8@IGFBP3
Hg19::chr7:45952690..45952701,-p21@IGFBP3
Hg19::chr7:45952705..45952723,-p9@IGFBP3
Hg19::chr7:45952772..45952808,+p@chr7:45952772..45952808
+
Hg19::chr7:45952836..45952875,+p@chr7:45952836..45952875
+
Hg19::chr7:45952925..45952936,-p14@IGFBP3
Hg19::chr7:45952960..45952978,-p16@IGFBP3
Hg19::chr7:45952985..45952996,-p19@IGFBP3
Hg19::chr7:45953003..45953022,-p17@IGFBP3
Hg19::chr7:45953004..45953071,+p@chr7:45953004..45953071
+
Hg19::chr7:45953044..45953078,-p2@IGFBP3
Hg19::chr7:45953080..45953100,-p7@IGFBP3
Hg19::chr7:45953092..45953099,+p@chr7:45953092..45953099
+
Hg19::chr7:45953113..45953132,-p13@IGFBP3
Hg19::chr7:45953149..45953156,-p24@IGFBP3
Hg19::chr7:45953152..45953169,+p@chr7:45953152..45953169
+
Hg19::chr7:45953215..45953229,-p@chr7:45953215..45953229
-
Hg19::chr7:45953243..45953254,-p@chr7:45953243..45953254
-
Hg19::chr7:45953266..45953277,-p@chr7:45953266..45953277
-
Hg19::chr7:45953287..45953301,-p@chr7:45953287..45953301
-
Hg19::chr7:45953320..45953329,+p@chr7:45953320..45953329
+
Hg19::chr7:45953339..45953442,-p@chr7:45953339..45953442
-
Hg19::chr7:45953356..45953389,+p@chr7:45953356..45953389
+
Hg19::chr7:45954407..45954428,+p@chr7:45954407..45954428
+
Hg19::chr7:45954422..45954464,-p4@IGFBP3
Hg19::chr7:45954467..45954535,-p6@IGFBP3
Hg19::chr7:45954480..45954494,+p@chr7:45954480..45954494
+
Hg19::chr7:45954539..45954548,-p27@IGFBP3
Hg19::chr7:45956182..45956215,+p@chr7:45956182..45956215
+
Hg19::chr7:45956182..45956271,-p5@IGFBP3
Hg19::chr7:45956222..45956246,+p@chr7:45956222..45956246
+
Hg19::chr7:45956805..45956831,+p@chr7:45956805..45956831
+
Hg19::chr7:45956835..45956852,-p@chr7:45956835..45956852
-
Hg19::chr7:45956836..45956919,+p@chr7:45956836..45956919
+
Hg19::chr7:45956856..45957005,-p3@IGFBP3
Hg19::chr7:45956931..45956944,+p@chr7:45956931..45956944
+
Hg19::chr7:45956964..45956971,+p@chr7:45956964..45956971
+
Hg19::chr7:45956988..45956995,+p@chr7:45956988..45956995
+
Hg19::chr7:45957006..45957009,+p@chr7:45957006..45957009
+
Hg19::chr7:45957011..45957025,-p15@IGFBP3
Hg19::chr7:45957026..45957035,-p28@IGFBP3
Hg19::chr7:45960456..45960484,+p@chr7:45960456..45960484
+
Hg19::chr7:45960675..45960686,+p@chr7:45960675..45960686
+
Hg19::chr7:45960863..45960877,-p1@IGFBP3


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:0008160protein tyrosine phosphatase activator activity0.0107528462670886
GO:0045663positive regulation of myoblast differentiation0.0107528462670886
GO:0045661regulation of myoblast differentiation0.0107528462670886
GO:0033239negative regulation of amine metabolic process0.0107528462670886
GO:0001933negative regulation of protein amino acid phosphorylation0.0107528462670886
GO:0045763negative regulation of amino acid metabolic process0.0107528462670886
GO:0019211phosphatase activator activity0.0126724377484379
GO:0045445myoblast differentiation0.0236762645983259
GO:0005520insulin-like growth factor binding0.0236762645983259
GO:0048741skeletal muscle fiber development0.0236762645983259
GO:0048747muscle fiber development0.0236762645983259
GO:0001932regulation of protein amino acid phosphorylation0.0236762645983259
GO:0033238regulation of amine metabolic process0.0236762645983259
GO:0042692muscle cell differentiation0.0236762645983259
GO:0006521regulation of amino acid metabolic process0.0236762645983259
GO:0045597positive regulation of cell differentiation0.0236762645983259
GO:0042493response to drug0.0252709154337371
GO:0042325regulation of phosphorylation0.0252709154337371
GO:0007519skeletal muscle development0.0252709154337371
GO:0051094positive regulation of developmental process0.0252709154337371
GO:0051174regulation of phosphorus metabolic process0.0252709154337371
GO:0019220regulation of phosphate metabolic process0.0252709154337371
GO:0019888protein phosphatase regulator activity0.0275241544507314
GO:0019208phosphatase regulator activity0.0275241544507314
GO:0014706striated muscle development0.0275729500161464
GO:0019838growth factor binding0.0275729500161464
GO:0009968negative regulation of signal transduction0.0310198813992766
GO:0045595regulation of cell differentiation0.0413922342778986
GO:0001558regulation of cell growth0.0449485937362989
GO:0007517muscle development0.0461256189118645



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
fibroblast9.85e-1576
skin fibroblast1.91e-1223
GAG secreting cell6.41e-109
carbohydrate secreting cell6.41e-109
stromal cell4.77e-0928
preadipocyte5.85e-0912
collagen secreting cell3.40e-086
chondroblast3.40e-086
chondrocyte3.40e-086
extracellular matrix secreting cell5.95e-0715
Uber Anatomy
Ontology termp-valuen
cavity lining7.98e-1012
serous membrane7.98e-1012
omentum8.72e-106
peritoneum8.72e-106
abdominal cavity8.72e-106
visceral peritoneum8.72e-106
extraembryonic membrane5.83e-0814
membranous layer5.83e-0814
chorion1.14e-077
skin of body2.62e-0741
integument6.37e-0746
integumental system6.37e-0746
Disease
Ontology termp-valuen
musculoskeletal system disease1.52e-095
myotonic disease1.52e-095
muscle tissue disease1.52e-095
myopathy1.52e-095
muscular disease1.52e-095
myotonic dystrophy1.52e-095


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)
MA0003.14.59841e-09
MA0004.10.0132867
MA0006.10.304319
MA0007.10.0109401
MA0009.10.188448
MA0014.14.74854e-06
MA0017.10.0179829
MA0019.10.0442103
MA0024.10.129538
MA0025.10.757843
MA0027.11.62682
MA0028.10.0130864
MA0029.10.431779
MA0030.10.133607
MA0031.10.101986
MA0038.10.0322832
MA0040.13.44917
MA0041.12.14144
MA0042.11.11645
MA0043.10.18864
MA0046.10.181878
MA0048.10.0419059
MA0050.11.12087
MA0051.12.75428
MA0052.10.444937
MA0055.10.71824
MA0056.10
MA0057.10.0182582
MA0058.11.01136
MA0059.10.00419321
MA0060.19.59188e-05
MA0061.10.0446599
MA0063.10
MA0066.10.0323854
MA0067.10.415509
MA0068.10.000102572
MA0069.10.179575
MA0070.10.17296
MA0071.10.472244
MA0072.10.170332
MA0073.12.07793e-11
MA0074.10.0311065
MA0076.10.00530197
MA0077.10.165866
MA0078.11.2439
MA0081.10.305597
MA0083.10.193036
MA0084.10.572572
MA0087.10.16891
MA0088.10.177493
MA0089.10
MA0090.13.34067
MA0091.10.0646989
MA0092.10.460399
MA0093.10.00161933
MA0095.10
MA0098.10
MA0100.10.0357081
MA0101.10.0113418
MA0103.10.0800113
MA0105.13.09803e-05
MA0106.19.17719
MA0107.10.0125785
MA0108.21.64982
MA0109.10
MA0111.10.648566
MA0113.10.047923
MA0114.10.00272901
MA0115.10.355528
MA0116.10.00327449
MA0117.10.608162
MA0119.10.0198925
MA0122.10.228629
MA0124.10.86615
MA0125.10.263758
MA0130.10
MA0131.10.0664674
MA0132.10
MA0133.10
MA0135.10.207272
MA0136.10.136702
MA0139.10.00145258
MA0140.10.0233094
MA0141.10.718361
MA0142.10.0879648
MA0143.11.5566
MA0144.10.00197784
MA0145.10.0281372
MA0146.10.00471804
MA0147.10.415627
MA0148.10.198277
MA0149.10.0214733
MA0062.20.00645693
MA0035.20.0231722
MA0039.25.23571e-07
MA0138.20.060442
MA0002.20.569636
MA0137.20.0143463
MA0104.20.0726509
MA0047.20.639922
MA0112.21.19916
MA0065.20.00014324
MA0150.10.205496
MA0151.10
MA0152.10.0246119
MA0153.10.252172
MA0154.10.421178
MA0155.10.00410503
MA0156.10.0491569
MA0157.10.265062
MA0158.10
MA0159.10.41813
MA0160.11.01106
MA0161.10
MA0162.16.64863e-07
MA0163.10.000138269
MA0164.11.14898
MA0080.20.03756
MA0018.20.0434893
MA0099.20.024684
MA0079.20
MA0102.20.605147
MA0258.10.102683
MA0259.10.854898
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

No analysis results for this cluster

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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