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Coexpression cluster:C198: Difference between revisions

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|pathway_enrichment=4.88436109433595e-05;0.00772950143178664;2;200;Focal adhesion (KEGG):04510!8.76239653607e-06;0.00184886566911077;2;85;ECM-receptor interaction (KEGG):04512!7.95242710836606e-06;0.00184886566911077;2;81;Protein digestion and absorption (KEGG):04974!5.10526184734612e-06;0.00184886566911077;2;65;Signaling by PDGF (Reactome):REACT_16888!8.58567593366187e-05;0.0107016695200294;2;265;Axon guidance (Reactome):REACT_18266!0.000101437625782269;0.0107016695200294;2;288;{ACTB,297} (Static Module):NA
|pathway_enrichment=4.88436109433595e-05;0.00772950143178664;2;200;Focal adhesion (KEGG):04510!8.76239653607e-06;0.00184886566911077;2;85;ECM-receptor interaction (KEGG):04512!7.95242710836606e-06;0.00184886566911077;2;81;Protein digestion and absorption (KEGG):04974!5.10526184734612e-06;0.00184886566911077;2;65;Signaling by PDGF (Reactome):REACT_16888!8.58567593366187e-05;0.0107016695200294;2;265;Axon guidance (Reactome):REACT_18266!0.000101437625782269;0.0107016695200294;2;288;{ACTB,297} (Static Module):NA
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|tfbs_overrepresentation_for_novel_motifs=0.99405,5.26664,0.948596,0.00654425,0.0311976,0.100928,0.581993,0.401868,3.0362,0.302132,0.313881,0.0208895,0.397797,2.95295,0.227475,1.07863,0.883041,0.434607,9.11399,2.12021,1.21964,2.37448,0.364327,0.493724,0.0937474,0.486529,10.5983,5.48138,0.0113188,1.56101,0.655037,0.279044,0.425959,1.47066,3.1237,1.14999,0.0407194,0.605166,0.058372,0.213772,0.000126952,1.79651,2.30614,2.07537,6.93556,0.635361,0.350185,1.28246,2.72956,1.20684,0.116418,0.373437,1.73211,0.368644,0.197841,0.841682,0.0348957,0.46919,1.79216,0.131475,0.668245,0.0689366,2.38521,1.22628,0.201546,0.0478078,0.254391,0.538929,0.0777074,0.405591,0.109772,0.0822715,0.00175561,0.196629,0.127035,1.41976,0.860108,0.0530684,0.0764645,0.467618,0.0746813,0.211393,0.0172683,0.0420966,0.166572,2.61646,0.0643886,0.36304,0.135703,0.625088,0.31994,0.151692,0.0885335,0.00684609,0.0717034,0.0996707,0.109218,0.347417,0.929714,0.09183,0.0107405,0.0862205,0.104483,0.0692392,0.170275,2.50498,0.4931,0.0596715,0.0109944,0.194115,0.376081,0.103243,0.0192795,0.533901,0.285548,0.0815904,1.48543,0.435441,0.40098,0.823434,0.191644,0.133837,0.0336868,0.677013,0.366795,2.16992,0.0639001,1.05202,0.217868,0.0536927,0.152065,0.147098,0.227028,0.666967,0.329397,0.672255,0.136268,0.0315274,0.298601,1.04623,0.671632,0.27242,0.0647711,0.699109,0.388555,0.986158,0.0404853,0.895108,0.38357,0.316319,9.54769,0.0131418,0.152271,0.350996,0.0686821,0.429938,0.030024,1.63131,0.185236,0.00720498,0.271582,0.438791,0.263431,0.255726,1.12365,0.0781068,1.33035,0.174728,4.63836
}}
}}

Revision as of 13:45, 26 November 2012


Full id: C198_Mesenchymal_Hair_Hepatic_Fibroblast_Smooth_tenocyte_Pericytes



Phase1 CAGE Peaks

Hg19::chr15:74468156..74468168,+p@chr15:74468156..74468168
+
Hg19::chr21:47401650..47401692,+p1@COL6A1
Hg19::chr21:47402595..47402613,+p@chr21:47402595..47402613
+
Hg19::chr21:47404171..47404205,+p@chr21:47404171..47404205
+
Hg19::chr21:47404201..47404227,-p@chr21:47404201..47404227
-
Hg19::chr21:47404207..47404295,+p@chr21:47404207..47404295
+
Hg19::chr21:47404302..47404340,+p@chr21:47404302..47404340
+
Hg19::chr21:47404327..47404375,-p@chr21:47404327..47404375
-
Hg19::chr21:47406434..47406447,+p@chr21:47406434..47406447
+
Hg19::chr21:47406480..47406493,-p@chr21:47406480..47406493
-
Hg19::chr21:47406517..47406541,+p6@COL6A1
Hg19::chr21:47406543..47406568,+p5@COL6A1
Hg19::chr21:47406856..47406869,+p15@COL6A1
Hg19::chr21:47406885..47406955,+p2@COL6A1
Hg19::chr21:47406935..47406993,-p@chr21:47406935..47406993
-
Hg19::chr21:47407540..47407554,-p@chr21:47407540..47407554
-
Hg19::chr21:47408990..47409018,+p@chr21:47408990..47409018
+
Hg19::chr21:47409532..47409537,+p@chr21:47409532..47409537
+
Hg19::chr21:47409561..47409573,-p@chr21:47409561..47409573
-
Hg19::chr21:47409685..47409693,-p@chr21:47409685..47409693
-
Hg19::chr21:47410165..47410170,+p@chr21:47410165..47410170
+
Hg19::chr21:47410279..47410304,+p@chr21:47410279..47410304
+
Hg19::chr21:47410688..47410701,+p@chr21:47410688..47410701
+
Hg19::chr21:47410932..47410962,-p@chr21:47410932..47410962
-
Hg19::chr21:47412107..47412140,-p@chr21:47412107..47412140
-
Hg19::chr21:47418034..47418040,+p@chr21:47418034..47418040
+
Hg19::chr21:47418307..47418324,+p@chr21:47418307..47418324
+
Hg19::chr21:47418813..47418822,+p3@COL6A1
Hg19::chr21:47421885..47421916,+p9@COL6A1
Hg19::chr21:47421929..47421942,+p19@COL6A1
Hg19::chr21:47422170..47422205,+p4@COL6A1
Hg19::chr21:47422241..47422263,+p7@COL6A1
Hg19::chr21:47422530..47422542,+p13@COL6A1
Hg19::chr21:47423457..47423466,+p@chr21:47423457..47423466
+
Hg19::chr21:47423500..47423511,+p@chr21:47423500..47423511
+
Hg19::chr21:47423769..47423786,+p@chr21:47423769..47423786
+
Hg19::chr21:47423911..47423979,+p@chr21:47423911..47423979
+
Hg19::chr21:47423986..47424046,-p@chr21:47423986..47424046
-
Hg19::chr21:47424225..47424238,+p@chr21:47424225..47424238
+
Hg19::chr21:47424253..47424260,+p@chr21:47424253..47424260
+
Hg19::chr21:47424266..47424304,+p@chr21:47424266..47424304
+
Hg19::chr21:47424373..47424395,+p@chr21:47424373..47424395
+
Hg19::chr21:47424418..47424444,+p@chr21:47424418..47424444
+
Hg19::chr21:47424561..47424570,+p@chr21:47424561..47424570
+
Hg19::chr21:47424604..47424616,+p@chr21:47424604..47424616
+
Hg19::chr21:47424675..47424687,+p@chr21:47424675..47424687
+
Hg19::chr21:47518016..47518071,+p1@COL6A2
Hg19::chr21:47518637..47518688,+p2@COL6A2
Hg19::chr21:47518695..47518709,+p6@COL6A2
Hg19::chr21:47531348..47531389,+p10@COL6A2
Hg19::chr21:47531422..47531446,+p14@COL6A2
Hg19::chr21:47531453..47531471,+p13@COL6A2
Hg19::chr21:47531482..47531512,-p@chr21:47531482..47531512
-
Hg19::chr21:47531911..47531959,-p@chr21:47531911..47531959
-
Hg19::chr21:47531929..47531974,+p12@COL6A2
Hg19::chr21:47532028..47532078,+p4@COL6A2
Hg19::chr21:47532083..47532106,+p11@COL6A2
Hg19::chr21:47532107..47532192,+p5@COL6A2
Hg19::chr21:47532226..47532238,+p28@COL6A2
Hg19::chr21:47532285..47532298,+p18@COL6A2
Hg19::chr21:47532318..47532355,+p8@COL6A2
Hg19::chr21:47532365..47532492,-p@chr21:47532365..47532492
-
Hg19::chr21:47532366..47532425,+p3@COL6A2
Hg19::chr21:47535780..47535815,+p17@COL6A2
Hg19::chr21:47535916..47535938,+p21@COL6A2
Hg19::chr21:47536285..47536294,+p@chr21:47536285..47536294
+
Hg19::chr21:47539710..47539714,+p@chr21:47539710..47539714
+
Hg19::chr21:47540424..47540442,+p27@COL6A2
Hg19::chr21:47542827..47542859,-p@chr21:47542827..47542859
-
Hg19::chr21:47545494..47545526,-p@chr21:47545494..47545526
-
Hg19::chr21:47545703..47545747,+p15@COL6A2
Hg19::chr21:47545788..47545804,+p42@COL6A2
Hg19::chr21:47545812..47545838,+p22@COL6A2
Hg19::chr21:47545905..47545936,+p23@COL6A2
Hg19::chr21:47545938..47545951,+p19@COL6A2
Hg19::chr21:47545961..47545972,+p37@COL6A2
Hg19::chr21:47546004..47546019,+p26@COL6A2
Hg19::chr21:47546031..47546052,+p29@COL6A2
Hg19::chr21:47546401..47546428,+p40@COL6A2
Hg19::chr21:47549257..47549279,+p44@COL6A2
Hg19::chr21:47551929..47551951,+p24@COL6A2
Hg19::chr21:47551979..47551997,+p20@COL6A2
Hg19::chr21:47552005..47552020,+p7@COL6A2
Hg19::chr21:47552113..47552127,+p36@COL6A2


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

p.valueFDRnGenesnPathwayName
4.88436109433595e-050.007729501431786642200Focal adhesion (KEGG):04510
8.76239653607e-060.00184886566911077285ECM-receptor interaction (KEGG):04512
7.95242710836606e-060.00184886566911077281Protein digestion and absorption (KEGG):04974
5.10526184734612e-060.00184886566911077265Signaling by PDGF (Reactome):REACT_16888
8.58567593366187e-050.01070166952002942265Axon guidance (Reactome):REACT_18266
0.0001014376257822690.01070166952002942288{ACTB,297} (Static Module):NA



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:0006817phosphate transport0.000475071195691557
GO:0015698inorganic anion transport0.000787730087606359
GO:0006820anion transport0.000794760467509113
GO:0005589collagen type VI0.000794760467509113
GO:0005578proteinaceous extracellular matrix0.000827362245860152
GO:0030934anchoring collagen0.00238403574865387
GO:0044421extracellular region part0.00239321462513256
GO:0022610biological adhesion0.00239321462513256
GO:0007155cell adhesion0.00239321462513256
GO:0006811ion transport0.00434955216285057
GO:0030198extracellular matrix organization and biogenesis0.00664278275475231
GO:0005581collagen0.0071473696355446
GO:0043062extracellular structure organization and biogenesis0.0102583545846563
GO:0030674protein binding, bridging0.0103183517189704
GO:0005201extracellular matrix structural constituent0.012989492507796
GO:0044420extracellular matrix part0.012989492507796
GO:0006810transport0.0222181450900092
GO:0051234establishment of localization0.0222181450900092
GO:0051179localization0.0247191580527521
GO:0016337cell-cell adhesion0.0274381479679809



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
somite4.61e-2971
presomitic mesoderm4.61e-2971
presumptive segmental plate4.61e-2971
dermomyotome4.61e-2971
trunk paraxial mesoderm4.61e-2971
dense mesenchyme tissue5.49e-2973
paraxial mesoderm2.92e-2872
presumptive paraxial mesoderm2.92e-2872
muscle tissue2.40e-2464
musculature2.40e-2464
musculature of body2.40e-2464
multilaminar epithelium5.66e-2483
epithelial vesicle6.11e-2478
skeletal muscle tissue6.15e-2462
striated muscle tissue6.15e-2462
myotome6.15e-2462
trunk mesenchyme2.74e-19122
mesenchyme2.38e-18160
entire embryonic mesenchyme2.38e-18160
integument1.97e-1146
integumental system1.97e-1146
unilaminar epithelium3.27e-11148
surface structure8.88e-1199
adipose tissue1.14e-1014
mesoderm3.00e-10315
mesoderm-derived structure3.00e-10315
presumptive mesoderm3.00e-10315
trunk4.03e-10199
organism subdivision1.09e-09264
splanchnic layer of lateral plate mesoderm4.15e-0983
artery7.45e-0942
arterial blood vessel7.45e-0942
arterial system7.45e-0942
systemic artery7.53e-0933
systemic arterial system7.53e-0933
skin of body1.58e-0841
smooth muscle tissue1.56e-0715
connective tissue2.29e-07371
vasculature4.36e-0778
vascular system4.36e-0778
musculoskeletal system6.37e-07167
Disease
Ontology termp-valuen
ovarian cancer6.21e-0714


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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