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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.454486775985259,0

Latest revision as of 11:26, 17 September 2013


Full id: C582_Smooth_tenocyte_mesenchymal_leiomyoma_Fibroblast_Olfactory_Aortic



Phase1 CAGE Peaks

Hg19::chr10:33200555..33200575,-p1@AF086249
Hg19::chr10:33200591..33200603,-p2@AF086249
Hg19::chr10:33200884..33200910,+p@chr10:33200884..33200910
+
Hg19::chr10:33200984..33201060,-p5@ITGB1
Hg19::chr10:33211224..33211280,-p@chr10:33211224..33211280
-
Hg19::chr10:33212555..33212600,-p9@ITGB1
Hg19::chr10:33212601..33212662,-p6@ITGB1
Hg19::chr10:33217106..33217178,-p@chr10:33217106..33217178
-
Hg19::chr10:33218785..33218853,-p@chr10:33218785..33218853
-
Hg19::chr10:33218882..33218915,-p@chr10:33218882..33218915
-
Hg19::chr10:33218945..33218966,-p@chr10:33218945..33218966
-
Hg19::chr10:33221480..33221527,-p7@ITGB1
Hg19::chr19:14732681..14732704,-p@chr19:14732681..14732704
-
Hg19::chr7:128410308..128410334,+p@chr7:128410308..128410334
+
Hg19::chr7:128410396..128410415,+p@chr7:128410396..128410415
+


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:0031594neuromuscular junction0.0102437301306959
GO:0042383sarcolemma0.0136583068409278
GO:0001726ruffle0.0144462860817506
GO:0008305integrin complex0.0144462860817506
GO:0031252leading edge0.0144462860817506
GO:0006968cellular defense response0.0144462860817506
GO:0048770pigment granule0.0144462860817506
GO:0042470melanosome0.0144462860817506
GO:0007229integrin-mediated signaling pathway0.0144462860817506
GO:0007160cell-matrix adhesion0.0144462860817506
GO:0031589cell-substrate adhesion0.0144462860817506
GO:0046982protein heterodimerization activity0.0144462860817506
GO:0043235receptor complex0.0144462860817506
GO:0007156homophilic cell adhesion0.0251215286538494
GO:0016477cell migration0.0265198791161348
GO:0042995cell projection0.0284300626091052
GO:0016023cytoplasmic membrane-bound vesicle0.0284300626091052
GO:0016337cell-cell adhesion0.0284300626091052
GO:0031988membrane-bound vesicle0.0284300626091052
GO:0042802identical protein binding0.0284300626091052
GO:0046983protein dimerization activity0.0284300626091052
GO:0051674localization of cell0.0284300626091052
GO:0006928cell motility0.0284300626091052
GO:0031410cytoplasmic vesicle0.0295019427764041
GO:0031982vesicle0.0295019427764041
GO:0006952defense response0.0383483230533743



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
fibroblast7.64e-1476
animal cell4.66e-11679
eukaryotic cell4.66e-11679
muscle precursor cell8.57e-0958
myoblast8.57e-0958
multi-potent skeletal muscle stem cell8.57e-0958
embryonic cell8.60e-08250
muscle cell8.83e-0855
mesodermal cell1.03e-07121
skin fibroblast1.40e-0723
electrically responsive cell3.92e-0761
electrically active cell3.92e-0761
somatic cell3.92e-07588
preadipocyte4.48e-0712
vascular associated smooth muscle cell5.32e-0732
smooth muscle cell7.33e-0743
smooth muscle myoblast7.33e-0743
Disease
Ontology termp-valuen
ovarian cancer8.15e-0914


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)
MA0003.15.0016e-06
MA0004.10.256222
MA0006.10.137644
MA0007.10.241375
MA0009.10.669377
MA0014.10.000336449
MA0017.10.16476
MA0019.11.75672
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.10.588958
MA0030.11.41545
MA0031.10.518602
MA0038.11.62076
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.10.669676
MA0046.10.659066
MA0048.10.0212749
MA0050.11.27601
MA0051.11.60805
MA0052.10.598036
MA0055.10.229721
MA0056.10
MA0057.10.0196406
MA0058.10.182945
MA0059.10.182001
MA0060.10.51173
MA0061.10.198509
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.0373092
MA0069.10.655419
MA0070.10.644843
MA0071.11.50438
MA0072.10.640598
MA0073.15.61316e-08
MA0074.10.894848
MA0076.10.194691
MA0077.10.633326
MA0078.11.90704
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.00789138
MA0089.10
MA0090.10.593146
MA0091.10.258318
MA0092.10.228476
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.10.141917
MA0103.10.411001
MA0105.10.0162551
MA0106.10.37688
MA0107.10.0950422
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.10.0920489
MA0115.10.900969
MA0116.10.0971018
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.11.83487
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.0481205
MA0140.10.30631
MA0141.10.180729
MA0142.11.2271
MA0143.11.79503
MA0144.11.00343
MA0145.10.00981909
MA0146.10.000217915
MA0147.10.0991954
MA0148.10.276339
MA0149.10.298252
MA0062.20.0512998
MA0035.20.305721
MA0039.20.000100247
MA0138.20.425279
MA0002.20.480166
MA0137.23.5699
MA0104.20.0667907
MA0047.20.366327
MA0112.20.124752
MA0065.20.0103297
MA0150.10.201098
MA0151.10
MA0152.10.838393
MA0153.11.80147
MA0154.10.0156321
MA0155.10.0077078
MA0156.10.469333
MA0157.10.46471
MA0158.10
MA0159.10.327637
MA0160.10.288813
MA0161.10
MA0162.10.000900738
MA0163.10.00038862
MA0164.10.402162
MA0080.20.139746
MA0018.20.378086
MA0099.20.312108
MA0079.22.98508e-13
MA0102.21.1957
MA0258.10.569952
MA0259.10.104286
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

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

TF#promotersEnrichmentp-valueq-value
GATA1#262354.520102714600150.003491678030095980.0177341517183871



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.

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