Personal tools

Coexpression cluster:C349: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.188938360773272,0

Latest revision as of 11:20, 17 September 2013


Full id: C349_Mesothelial_Fibroblast_Preadipocyte_Ewing_mesenchymal_Skeletal_Smooth



Phase1 CAGE Peaks

Hg19::chr13:38138680..38138703,-p6@POSTN
Hg19::chr13:38143509..38143522,-p@chr13:38143509..38143522
-
Hg19::chr13:38143906..38143926,-p5@POSTN
Hg19::chr13:38143952..38143964,-p13@POSTN
Hg19::chr13:38144751..38144809,-p4@POSTN
Hg19::chr13:38145530..38145539,-p8@POSTN
Hg19::chr13:38145556..38145571,-p3@POSTN
Hg19::chr13:38145589..38145600,-p12@POSTN
Hg19::chr13:38148231..38148243,-p@chr13:38148231..38148243
-
Hg19::chr13:38151913..38151938,-p1@AK023481
Hg19::chr13:38153005..38153062,-p@chr13:38153005..38153062
-
Hg19::chr13:38153184..38153228,-p@chr13:38153184..38153228
-
Hg19::chr13:38153245..38153265,-p@chr13:38153245..38153265
-
Hg19::chr13:38153407..38153451,-p@chr13:38153407..38153451
-
Hg19::chr13:38153485..38153498,-p@chr13:38153485..38153498
-
Hg19::chr13:38154048..38154108,-p@chr13:38154048..38154108
-
Hg19::chr13:38154109..38154139,-p@chr13:38154109..38154139
-
Hg19::chr13:38154735..38154791,-p2@POSTN
Hg19::chr13:38154792..38154807,-p10@POSTN
Hg19::chr13:38156527..38156539,-p3@AK297914
Hg19::chr13:38156549..38156595,-p1@AK297914
Hg19::chr13:38156622..38156656,-p2@AK297914
Hg19::chr13:38158135..38158197,-p@chr13:38158135..38158197
-
Hg19::chr13:38158993..38159017,-p@chr13:38158993..38159017
-
Hg19::chr13:38160326..38160357,-p@chr13:38160326..38160357
-
Hg19::chr13:38160359..38160428,-p@chr13:38160359..38160428
-
Hg19::chr13:38161054..38161069,-p@chr13:38161054..38161069
-
Hg19::chr13:38164537..38164581,-p@chr13:38164537..38164581
-
Hg19::chr13:38164609..38164645,-p@chr13:38164609..38164645
-
Hg19::chr13:38166252..38166258,+p@chr13:38166252..38166258
+
Hg19::chr13:38171411..38171427,-p@chr13:38171411..38171427
-
Hg19::chr13:38172896..38172911,-p1@POSTN


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:0008201heparin binding0.0158880843047215
GO:0005539glycosaminoglycan binding0.0158880843047215
GO:0030247polysaccharide binding0.0158880843047215
GO:0001871pattern binding0.0158880843047215
GO:0001501skeletal development0.020917225950783
GO:0005578proteinaceous extracellular matrix0.0341709979647104
GO:0030246carbohydrate binding0.0341709979647104
GO:0044421extracellular region part0.0480395619922289
GO:0022610biological adhesion0.0480395619922289
GO:0007155cell adhesion0.0480395619922289



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
skeletal muscle tissue1.78e-1562
striated muscle tissue1.78e-1562
myotome1.78e-1562
muscle tissue1.24e-1464
musculature1.24e-1464
musculature of body1.24e-1464
dense mesenchyme tissue1.67e-1273
somite4.27e-1271
presomitic mesoderm4.27e-1271
presumptive segmental plate4.27e-1271
dermomyotome4.27e-1271
trunk paraxial mesoderm4.27e-1271
paraxial mesoderm8.89e-1272
presumptive paraxial mesoderm8.89e-1272
epithelial vesicle4.62e-1078
heart8.90e-1024
primitive heart tube8.90e-1024
primary heart field8.90e-1024
anterior lateral plate mesoderm8.90e-1024
heart tube8.90e-1024
heart primordium8.90e-1024
cardiac mesoderm8.90e-1024
cardiogenic plate8.90e-1024
heart rudiment8.90e-1024
artery1.70e-0942
arterial blood vessel1.70e-0942
arterial system1.70e-0942
splanchnic layer of lateral plate mesoderm2.60e-0983
multilaminar epithelium7.54e-0983
primary circulatory organ3.63e-0827
systemic artery3.18e-0733
systemic arterial system3.18e-0733
cardiovascular system9.86e-07109
Disease
Ontology termp-valuen
ovarian cancer8.87e-1114


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)
MA0003.11.26456e-11
MA0004.10.085298
MA0006.10.0278021
MA0007.10.0768943
MA0009.10.395891
MA0014.11.0021e-07
MA0017.10.0388023
MA0019.10.165418
MA0024.10.312615
MA0025.10.508683
MA0027.11.93196
MA0028.10.032054
MA0029.10.873668
MA0030.10.853787
MA0031.10.270046
MA0038.10.138548
MA0040.10.332103
MA0041.12.17364
MA0042.10.969417
MA0043.10.39615
MA0046.11.0052
MA0048.10.000662255
MA0050.11.45038
MA0051.10.136135
MA0052.10.335128
MA0055.17.00754e-06
MA0056.10
MA0057.10.00430884
MA0058.10.0469637
MA0059.10.0465255
MA0060.10.00694078
MA0061.10.00444477
MA0063.10
MA0066.10.138793
MA0067.10.673046
MA0068.10.00211477
MA0069.10.998321
MA0070.10.978382
MA0071.10.752373
MA0072.10.371146
MA0073.18.67895e-16
MA0074.11.3502
MA0076.10.0525452
MA0077.12.56671
MA0078.11.71043
MA0081.10.176635
MA0083.10.40206
MA0084.11.97407
MA0087.10.966048
MA0088.10.0321423
MA0089.10
MA0090.10.461949
MA0091.10.292177
MA0092.10.0698409
MA0093.10.0285794
MA0095.10
MA0098.10
MA0100.10.146599
MA0101.10.029437
MA0103.10.108135
MA0105.10.000377448
MA0106.10.163029
MA0107.10.0137208
MA0108.20.738478
MA0109.10
MA0111.10.490476
MA0113.10.173209
MA0114.10.0617658
MA0115.10.603788
MA0116.10.0672762
MA0117.10.427006
MA0119.10.0412526
MA0122.10.44876
MA0124.13.48898
MA0125.10.493194
MA0130.10
MA0131.10.2093
MA0132.10
MA0133.10
MA0135.10.420972
MA0136.10.142619
MA0139.10.00355142
MA0140.11.22262
MA0141.10.17465
MA0142.10.690612
MA0143.10.515444
MA0144.10.144799
MA0145.10.00119262
MA0146.13.96847e-08
MA0147.10.0149049
MA0148.10.0971411
MA0149.10.110599
MA0062.20.004042
MA0035.20.744315
MA0039.23.88221e-11
MA0138.20.198014
MA0002.20.0316769
MA0137.20.581971
MA0104.20.00686015
MA0047.20.155654
MA0112.20.000100843
MA0065.20.00131177
MA0150.10.204231
MA0151.10
MA0152.11.81395
MA0153.11.20388
MA0154.10.145314
MA0155.17.84258e-05
MA0156.10.138397
MA0157.10.645687
MA0158.10
MA0159.10.0700275
MA0160.10.695992
MA0161.10
MA0162.18.1789e-07
MA0163.11.36276e-07
MA0164.10.181076
MA0080.20.0286016
MA0018.20.163878
MA0099.20.379875
MA0079.20
MA0102.20.88257
MA0258.10.00945121
MA0259.10.0164145
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

This analysis result is provided for C0 - C305 clusters.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C349&oldid=3067466"