Personal tools

Coexpression cluster:C773: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.13906568410137,0.807822484041843,0.989615364648447,0.944824287079112,0,0,0,0,0,0,0,0,0,0,0,0,0,0.114346030083907,0,0,0,0,0,0,0,0,0,0,0,0,0.0943257785523457,0.165795549095301,0,0.28535904381024,0.109812129893149,0,0.092187879276543,0.435163799767044,0.216293844171574,0.371855321441455,0.0749050231308192,0,0.0880380456512581,0.403192519147754,0.120879483793741,0.357682244950033,0,0,0,0.728608486331722,0.329351182440039,0.675497287323882,0,0,0.0853579634813876,0.534228984731047,0.239688610815101,0.507212952056032,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.388413235858955,0,0.413854720847808,0,0.172204315337917,0.0752072885286432,0.0869750240711818,0.0365629421359175,0,0,0,0,0,0,0,0,0,0,0,0,0,0.152135224370875,0.105550390723108,0.0824244927467616,0.0998244934409575,0,0,0.147004833432507,0,0.0948420448069823,0.135979123430744,0.257712632750166,0.0371473953017556,0,0,0,0,0,0.365076740692652,0,0,0,0.098041533233204,0.14526713795306,0.109523411542048,0.131832994540557,0,0.623504608603281,0.298125776038763,0,0.344862874141306,0.0657521671341522,0.0612101670326939,0,0,0,0,0,0,0,0,0.0806820944291313,0,0.0427037663627782,0.340047884800798,0.29864956877975,0,0,0,0,0,0,0,0.312106748713396,0.162483374261274,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.141926672950355,0.373597977997133,0.109512603169101,0,0,0,0,0,0,0.409001911408146,0.215701246001134,0,0.62844773426536,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0687674306079092,0.123606948733483,0,0.0416014802313693,0,0,0,0,0.0476371106609188,0,0.635526802013318,0.924680729861736,0.925307549289423,0,0,0.0955936734149088,0,0,0.287205473226075,0.223217704226089,0.383411566635695,0.0372505621677013,0,0,0,0,0,0,0,0.0267366343438753,0,0,0,0.0425075842205678,0,0,0,0,0.0863651195885523,0.279872640127852,0,0,0,0,0,0,0,0,0,0,0,0,0.253326341486756,0.114423942847335,0,0,0,0,0,0,0,0,0.303944979097508,0.0811586845710415,0.0715362608323278,0,0,0,0,0,0,0,0,0,0.511485107029086,0.844056295477674,0.424499755566394,0.0502604313716981,0,0,0,0,0,0,0,0,0,0,0,0.0361830415099865,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.317952211644416,0.13197886088098,0.1739908434077,0.666029218334375,0.198946124308939,0,0.146442146711949,0,0.0472025886002021,0,0,0,0.0622173525481225,0,0,0.0831811723542952,0,0.127165533945345,0,0,0,0,0,0,0,0,0,0,0,0,0.0425916600387234,0,0,0,0.217499801210003,0.416114259418732,0.198663768922935,0.0622241049201175,0,0.0560798888033103,0,0,0.0355204411879812,0,0.174889423717366,0,0.179106597910867,0,0,0.118863773699242,0.714516149532692,0.835857791701318,0.762735136301336,0.72832658381254,0.750747883298177,0.723763148927142,0.137404238899705,0,0,0,0,0.413470135008,1.01784203074346,0.0718350632709503,0,0.0483689238882358,0.810160376260214,0.412477887232674,0.81133097716437,0,1.15849040705223,0.924047097377181,0,0.153575950653048,0,0.574821163849931,0.952369451339341,0.879483718777198,0,0,0.418845147443963,0.350111114970215,0.194067664482614,0,0,0.543658045689416,0,0.548179483820734,0.519179906623967,0,0,0.110140484268162,0,0,0.0390744040629657,0,0,0,0,0,0,0,0,0.14963850419244,0,0.187529586342753,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.614543284250757,0,0,0,0,0,0,0,0,0,0.0715216048933879,0,0,0,0,0,0,0,0,0,0,0.195613876017916,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0468626006398675,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.152898414163168,0.59529672537494,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0943943881882323,0,0,0,0,0,0,0,0,0,0,0,0,0.0695052016201444,0,0,0,0,0,0,0,0.0402022792589852,0,0,0,0.203072024846461,0,0,0.0334876163089719,0,0,0,0,0,0.0584468268118252,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0635628004819691,0.0222033657448865,0,0.473072292107485,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0634100406668813,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.196157017907754,0,0,0,0.203310140571095,0,0,0.075329031500352,0,0,0.451896997302179,0,0.702548332769612,1.02573931852979,0.697440262644215,1.13336282823709,0.501563326077312,0,0,0.409127188182498,0.0607951148206197,0.140132417719247,0.148254195206626,0.526860191865332,0.512633934281354,0,0.341293561984619,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.13615336353379,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.20749728713235,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.297242003065574,0,0,0,0,0,0,0,0,0,0.277457240448102,0,0,0,0,0,0,0,0,0,0,0.0458045054759181,0,0,0,0,0,0,0,0,0,0,0,0.0817850418435885,0,0,0,0.16829944338126,0.0988652163614907,0,0.227197610169401,0.209625657429162,0.291266468109506,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0748046823502985,0.0996224845265148,0,0.132614371326254,0,0,0,0,0,0,0,0,0,0.325512595891034,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0839445661171913,0,0,0,0.0461562834654493,0,0,0,0,0.0283076897745917,0.155437229153111,0,0.0339876779246108,0.154396393934003,0,0,0,0,0,0,0,0
|full_id=C773_Smooth_mesenchymal_Hair_Lymphatic_Preadipocyte_Aortic_anaplastic
|full_id=C773_Smooth_mesenchymal_Hair_Lymphatic_Preadipocyte_Aortic_anaplastic
|gostat_on_coexpression_clusters=GO:0008009!chemokine activity!0.0322890344084268!2919$GO:0042379!chemokine receptor binding!0.0322890344084268!2919$GO:0001664!G-protein-coupled receptor binding!0.0322890344084268!2919$GO:0042330!taxis!0.0322890344084268!2919$GO:0006935!chemotaxis!0.0322890344084268!2919$GO:0007626!locomotory behavior!0.0322890344084268!2919$GO:0008285!negative regulation of cell proliferation!0.0322890344084268!2919$GO:0030036!actin cytoskeleton organization and biogenesis!0.0322890344084268!2919$GO:0008083!growth factor activity!0.0322890344084268!2919$GO:0030029!actin filament-based process!0.0322890344084268!2919$GO:0006954!inflammatory response!0.0322890344084268!2919$GO:0007610!behavior!0.0322890344084268!2919$GO:0005125!cytokine activity!0.0322890344084268!2919$GO:0009611!response to wounding!0.0396907747556811!2919$GO:0008047!enzyme activator activity!0.0396907747556811!2919$GO:0042127!regulation of cell proliferation!0.0396907747556811!2919$GO:0005615!extracellular space!0.0419757447309549!2919$GO:0006952!defense response!0.0419757447309549!2919$GO:0042221!response to chemical stimulus!0.0419757447309549!2919$GO:0009605!response to external stimulus!0.0428558813140233!2919$GO:0007010!cytoskeleton organization and biogenesis!0.043859649122807!2919$GO:0007399!nervous system development!0.043859649122807!2919$GO:0008283!cell proliferation!0.043859649122807!2919
|gostat_on_coexpression_clusters=GO:0008009!chemokine activity!0.0322890344084268!2919$GO:0042379!chemokine receptor binding!0.0322890344084268!2919$GO:0001664!G-protein-coupled receptor binding!0.0322890344084268!2919$GO:0042330!taxis!0.0322890344084268!2919$GO:0006935!chemotaxis!0.0322890344084268!2919$GO:0007626!locomotory behavior!0.0322890344084268!2919$GO:0008285!negative regulation of cell proliferation!0.0322890344084268!2919$GO:0030036!actin cytoskeleton organization and biogenesis!0.0322890344084268!2919$GO:0008083!growth factor activity!0.0322890344084268!2919$GO:0030029!actin filament-based process!0.0322890344084268!2919$GO:0006954!inflammatory response!0.0322890344084268!2919$GO:0007610!behavior!0.0322890344084268!2919$GO:0005125!cytokine activity!0.0322890344084268!2919$GO:0009611!response to wounding!0.0396907747556811!2919$GO:0008047!enzyme activator activity!0.0396907747556811!2919$GO:0042127!regulation of cell proliferation!0.0396907747556811!2919$GO:0005615!extracellular space!0.0419757447309549!2919$GO:0006952!defense response!0.0419757447309549!2919$GO:0042221!response to chemical stimulus!0.0419757447309549!2919$GO:0009605!response to external stimulus!0.0428558813140233!2919$GO:0007010!cytoskeleton organization and biogenesis!0.043859649122807!2919$GO:0007399!nervous system development!0.043859649122807!2919$GO:0008283!cell proliferation!0.043859649122807!2919

Revision as of 18:29, 12 September 2012


Full id: C773_Smooth_mesenchymal_Hair_Lymphatic_Preadipocyte_Aortic_anaplastic



Phase1 CAGE Peaks

Hg19::chr4:74735102..74735117,+p1@CXCL1
Hg19::chr4:74735383..74735394,+p@chr4:74735383..74735394
+
Hg19::chr4:74735431..74735449,+p@chr4:74735431..74735449
+
Hg19::chr4:74735641..74735656,+p@chr4:74735641..74735656
+
Hg19::chr4:74736251..74736276,+p@chr4:74736251..74736276
+
Hg19::chr4:74736294..74736305,+p@chr4:74736294..74736305
+
Hg19::chr4:74736340..74736359,+p@chr4:74736340..74736359
+
Hg19::chr4:74736382..74736398,+p@chr4:74736382..74736398
+
Hg19::chr4:74736459..74736475,+p@chr4:74736459..74736475
+
Hg19::chr4:74736642..74736654,+p@chr4:74736642..74736654
+
Hg19::chr4:74810127..74810130,-p1@ENST00000502804


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:0008009chemokine activity0.0322890344084268
GO:0042379chemokine receptor binding0.0322890344084268
GO:0001664G-protein-coupled receptor binding0.0322890344084268
GO:0042330taxis0.0322890344084268
GO:0006935chemotaxis0.0322890344084268
GO:0007626locomotory behavior0.0322890344084268
GO:0008285negative regulation of cell proliferation0.0322890344084268
GO:0030036actin cytoskeleton organization and biogenesis0.0322890344084268
GO:0008083growth factor activity0.0322890344084268
GO:0030029actin filament-based process0.0322890344084268
GO:0006954inflammatory response0.0322890344084268
GO:0007610behavior0.0322890344084268
GO:0005125cytokine activity0.0322890344084268
GO:0009611response to wounding0.0396907747556811
GO:0008047enzyme activator activity0.0396907747556811
GO:0042127regulation of cell proliferation0.0396907747556811
GO:0005615extracellular space0.0419757447309549
GO:0006952defense response0.0419757447309549
GO:0042221response to chemical stimulus0.0419757447309549
GO:0009605response to external stimulus0.0428558813140233
GO:0007010cytoskeleton organization and biogenesis0.043859649122807
GO:0007399nervous system development0.043859649122807
GO:0008283cell proliferation0.043859649122807



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
cardiovascular system1.53e-26110
circulatory system2.66e-26113
vasculature1.42e-2579
vascular system1.42e-2579
vessel7.87e-2269
splanchnic layer of lateral plate mesoderm8.75e-2284
artery5.66e-2142
arterial blood vessel5.66e-2142
arterial system5.66e-2142
blood vessel3.48e-2060
epithelial tube open at both ends3.48e-2060
blood vasculature3.48e-2060
vascular cord3.48e-2060
epithelial tube5.78e-20118
anatomical system4.71e-19625
anatomical group1.10e-18626
multilaminar epithelium2.36e-1882
multi-cellular organism7.22e-18659
germ layer3.34e-17604
embryonic tissue3.34e-17604
presumptive structure3.34e-17604
epiblast (generic)3.34e-17604
mesoderm3.57e-17448
mesoderm-derived structure3.57e-17448
presumptive mesoderm3.57e-17448
embryonic structure4.44e-17605
developing anatomical structure4.44e-17605
systemic artery1.19e-1633
systemic arterial system1.19e-1633
embryo1.23e-16612
dermomyotome1.40e-1670
somite1.86e-1683
paraxial mesoderm1.86e-1683
presomitic mesoderm1.86e-1683
presumptive segmental plate1.86e-1683
trunk paraxial mesoderm1.86e-1683
presumptive paraxial mesoderm1.86e-1683
lateral plate mesoderm2.31e-16216
cell layer2.40e-16312
skeletal muscle tissue4.05e-1661
striated muscle tissue4.05e-1661
myotome4.05e-1661
trunk mesenchyme1.00e-15143
epithelium1.06e-15309
muscle tissue1.82e-1563
musculature1.82e-1563
musculature of body1.82e-1563
unilaminar epithelium7.21e-15138
anatomical cluster2.08e-13286
anatomical conduit2.22e-13241
musculoskeletal system1.28e-11167
multi-tissue structure1.29e-11347
trunk8.63e-11216
mesenchyme3.80e-10238
entire embryonic mesenchyme3.80e-10238
aorta3.33e-0921
aortic system3.33e-0921
tube9.87e-09194
organism subdivision1.47e-07365
blood vessel smooth muscle3.10e-0710
arterial system smooth muscle3.10e-0710
artery smooth muscle tissue3.10e-0710
aorta smooth muscle tissue3.10e-0710
compound organ3.85e-0769


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CEBPB#105153.623248920829460.0074439847494370.0307095245396765
POLR2A#5430101.952230160507340.00304073181841430.0161359174017261
STAT3#677454.781574998706470.002192062661377620.0126365751665076



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

This analysis result is provided for C0 - C305 clusters.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C773&oldid=2140148"