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Coexpression cluster:C223: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0.280667563736426,0.215452908500715,0.266167329895794,0.301189131856195,0.160456854061196,0.438491250631057,0,0,0,0.0954252957357428,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.098894583405387,1.36938708133118,1.11501473223758,1.16049032823397,0.254133631374496,0.835031874754131,0,0,0.0365629421359175,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.175213663176675,0.098041533233204,0,0.109523411542048,0,0.193313197142976,0.315443408671468,0.174157272143411,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.116105357238318,0,0,0.522713499186741,0.315505788884406,0.494059792163661,0.633569650252872,0.261124880180198,0.447698047811663,0.427332181064137,0.21766508996265,0.225841234395813,0.631610054221788,0.518678080863166,0,0.775984100479868,0.433415482641132,0.178597644615193,0,0,0,0,0,0,0,0,0,0,0.215701246001134,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.201612826790636,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0527984507438095,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0932902756138882,0,0,0.271536759545907,0.20855662473171,0.132938760828427,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.262897838155083,0.233938840156098,0.119059432222927,0.130791706039133,0,0,0,0,0.0734870933250891,0,0,0,0,0,0,0.114986933642873,0,0.114741150775265,0.241627012706536,0.116250315550445,0.265284977163665,0.179711634111168,0.306084857468188,0.171012795094276,0,0,0.13197886088098,0.0342782958079773,0,0.0907590042666714,0,0,0,0.0897740605496476,0,0.0535103765953433,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0425916600387234,0,0,0,0,0,0,0,0,0,0,0,0,0.0370406554214911,0,0,0,0,0,0.374623719925306,0,0,0,0,0.284796311279533,0.35947955275451,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.238332309002125,0,0,0,0,0.190714085371158,0.475717219026413,0.653946052550822,0,0,0.0802332713627146,0,0,0,0,0,0,0.548179483820734,0.422667707943698,0,0,0,0,0,0.0390744040629657,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0951833797824107,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.291141860941089,0.276667193547453,0.348040468312977,0,0,0,0,0,0.0789089986057754,0,0,0,0,0.776456617701592,0,0.0715216048933879,0,0,0,0,0,0,0,0,0,0,0,0,0.0921546695012139,0,0,0,0,0,0,0,0,0,0,0,0.0321956448428329,0,0,0,0,0.41413833263652,0.0730563942977996,0.414823712432763,0,0,0,0,0,0,0,0,0,0.065666642656593,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.129406115216345,0.0405993330353711,0,0,0.227358067595577,0,0,0,0,0,0,0,0,0,0,0,0,0.379970008661726,0,0,0,0,0,0,0,0,0.0421808920916863,0,0,0,0,0,0,0,0,0,0,0,0,0.0282390906884824,0.387603278412367,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.133083515879435,0,0,0,0.0983905284693096,0.31931413826482,0.270497510320477,0,0,0,0,0,0.0593938447453515,0,0,0,0.0685890998680107,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0912142501211956,0,0.139503167935131,0.176998219474839,0.276418423478184,0,0.205454389011787,0.117561082617775,0,0,0,0,0,0,0,0.0607951148206197,0.245909871574826,0,0,0,0,0.145536958608929,0,0.128203955531532,0.126050026678357,0,0,0,0,0.162388697080292,0,0,0.23460721171067,0.208871915315994,0,0,0.0766091494124484,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0837085814034122,0,0,0.11991684384043,0,0,0,0.116024799788948,0,0,0,0,0,0,0,0,0,0,0,0.129231191796032,0,0,0,0,0.0797978929983786,0,0,0,0,0,0,0,0,0,0,0,0,0.247131973414421,0,0,0,0,0.159420353662981,0,0,0,0,0,0,0,0,0,0,0.435752137030173,0.857981760202958,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0744901950284599,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.457760559026453,0,0.0271284845789754,0,0.186295585685449,0,0,0,0,0,0,0,0,0,0.137352534412557,0.576692994605879,0.500117427043148,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.124719478691449,0,0,0,0.103624360079764,0,0.0500863030838633,0,0,0,0
|full_id=C223_Chondrocyte_basal_renal_Fibroblast_Smooth_spindle_Synoviocyte
|full_id=C223_Chondrocyte_basal_renal_Fibroblast_Smooth_spindle_Synoviocyte
|gostat_on_coexpression_clusters=GO:0008160!protein tyrosine phosphatase activator activity!0.0107528462670886!3486$GO:0045663!positive regulation of myoblast differentiation!0.0107528462670886!3486$GO:0045661!regulation of myoblast differentiation!0.0107528462670886!3486$GO:0033239!negative regulation of amine metabolic process!0.0107528462670886!3486$GO:0001933!negative regulation of protein amino acid phosphorylation!0.0107528462670886!3486$GO:0045763!negative regulation of amino acid metabolic process!0.0107528462670886!3486$GO:0019211!phosphatase activator activity!0.0126724377484379!3486$GO:0045445!myoblast differentiation!0.0236762645983259!3486$GO:0005520!insulin-like growth factor binding!0.0236762645983259!3486$GO:0048741!skeletal muscle fiber development!0.0236762645983259!3486$GO:0048747!muscle fiber development!0.0236762645983259!3486$GO:0001932!regulation of protein amino acid phosphorylation!0.0236762645983259!3486$GO:0033238!regulation of amine metabolic process!0.0236762645983259!3486$GO:0042692!muscle cell differentiation!0.0236762645983259!3486$GO:0006521!regulation of amino acid metabolic process!0.0236762645983259!3486$GO:0045597!positive regulation of cell differentiation!0.0236762645983259!3486$GO:0042493!response to drug!0.0252709154337371!4363$GO:0042325!regulation of phosphorylation!0.0252709154337371!3486$GO:0007519!skeletal muscle development!0.0252709154337371!3486$GO:0051094!positive regulation of developmental process!0.0252709154337371!3486$GO:0051174!regulation of phosphorus metabolic process!0.0252709154337371!3486$GO:0019220!regulation of phosphate metabolic process!0.0252709154337371!3486$GO:0019888!protein phosphatase regulator activity!0.0275241544507314!3486$GO:0019208!phosphatase regulator activity!0.0275241544507314!3486$GO:0014706!striated muscle development!0.0275729500161464!3486$GO:0019838!growth factor binding!0.0275729500161464!3486$GO:0009968!negative regulation of signal transduction!0.0310198813992766!3486$GO:0045595!regulation of cell differentiation!0.0413922342778986!3486$GO:0001558!regulation of cell growth!0.0449485937362989!3486$GO:0007517!muscle development!0.0461256189118645!3486
|gostat_on_coexpression_clusters=GO:0008160!protein tyrosine phosphatase activator activity!0.0107528462670886!3486$GO:0045663!positive regulation of myoblast differentiation!0.0107528462670886!3486$GO:0045661!regulation of myoblast differentiation!0.0107528462670886!3486$GO:0033239!negative regulation of amine metabolic process!0.0107528462670886!3486$GO:0001933!negative regulation of protein amino acid phosphorylation!0.0107528462670886!3486$GO:0045763!negative regulation of amino acid metabolic process!0.0107528462670886!3486$GO:0019211!phosphatase activator activity!0.0126724377484379!3486$GO:0045445!myoblast differentiation!0.0236762645983259!3486$GO:0005520!insulin-like growth factor binding!0.0236762645983259!3486$GO:0048741!skeletal muscle fiber development!0.0236762645983259!3486$GO:0048747!muscle fiber development!0.0236762645983259!3486$GO:0001932!regulation of protein amino acid phosphorylation!0.0236762645983259!3486$GO:0033238!regulation of amine metabolic process!0.0236762645983259!3486$GO:0042692!muscle cell differentiation!0.0236762645983259!3486$GO:0006521!regulation of amino acid metabolic process!0.0236762645983259!3486$GO:0045597!positive regulation of cell differentiation!0.0236762645983259!3486$GO:0042493!response to drug!0.0252709154337371!4363$GO:0042325!regulation of phosphorylation!0.0252709154337371!3486$GO:0007519!skeletal muscle development!0.0252709154337371!3486$GO:0051094!positive regulation of developmental process!0.0252709154337371!3486$GO:0051174!regulation of phosphorus metabolic process!0.0252709154337371!3486$GO:0019220!regulation of phosphate metabolic process!0.0252709154337371!3486$GO:0019888!protein phosphatase regulator activity!0.0275241544507314!3486$GO:0019208!phosphatase regulator activity!0.0275241544507314!3486$GO:0014706!striated muscle development!0.0275729500161464!3486$GO:0019838!growth factor binding!0.0275729500161464!3486$GO:0009968!negative regulation of signal transduction!0.0310198813992766!3486$GO:0045595!regulation of cell differentiation!0.0413922342778986!3486$GO:0001558!regulation of cell growth!0.0449485937362989!3486$GO:0007517!muscle development!0.0461256189118645!3486

Revision as of 14:56, 12 September 2012


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><br>

Uber Anatomy
Ontology termp-valuen
trunk1.73e-12216
organism subdivision5.82e-12365
trunk mesenchyme1.01e-10143
mesenchyme1.18e-10238
entire embryonic mesenchyme1.18e-10238
epithelial tube2.18e-10118
muscle tissue3.67e-1063
musculature3.67e-1063
musculature of body3.67e-1063
skeletal muscle tissue4.45e-1061
striated muscle tissue4.45e-1061
myotome4.45e-1061
multi-cellular organism5.17e-10659
multi-tissue structure6.28e-10347
splanchnic layer of lateral plate mesoderm1.64e-0984
multilaminar epithelium1.15e-0882
dermomyotome1.17e-0870
artery3.62e-0842
arterial blood vessel3.62e-0842
arterial system3.62e-0842
anatomical cluster8.42e-08286
systemic artery8.71e-0833
systemic arterial system8.71e-0833
compound organ1.79e-0769
somite2.08e-0783
paraxial mesoderm2.08e-0783
presomitic mesoderm2.08e-0783
presumptive segmental plate2.08e-0783
trunk paraxial mesoderm2.08e-0783
presumptive paraxial mesoderm2.08e-0783
extraembryonic structure2.98e-0724
anatomical system3.74e-07625
extraembryonic membrane3.91e-0714
membranous layer3.91e-0714
anatomical group6.65e-07626


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)

{{{tfbs_overrepresentation_jaspar}}}



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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