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{{Coexpression_clusters
{
|full_id=C504_leiomyoma_Lens_Ciliary_mesenchymal_Smooth_Mesothelial_Renal

Latest revision as of 11:24, 17 September 2013


Full id: C504_leiomyoma_Lens_Ciliary_mesenchymal_Smooth_Mesothelial_Renal



Phase1 CAGE Peaks

Hg19::chr3:98515870..98515887,-p2@DCBLD2
Hg19::chr3:98515943..98515954,-p15@DCBLD2
Hg19::chr3:98516110..98516123,-p5@DCBLD2
Hg19::chr3:98516909..98516965,-p6@DCBLD2
Hg19::chr3:98516991..98517004,-p22@DCBLD2
Hg19::chr3:98517010..98517033,-p14@DCBLD2
Hg19::chr3:98517248..98517268,-p27@DCBLD2
Hg19::chr3:98517295..98517325,-p11@DCBLD2
Hg19::chr3:98517628..98517642,-p10@DCBLD2
Hg19::chr3:98517866..98517882,-p26@DCBLD2
Hg19::chr3:98518027..98518049,-p9@DCBLD2
Hg19::chr3:98518144..98518166,-p7@DCBLD2
Hg19::chr3:98518582..98518608,-p@chr3:98518582..98518608
-
Hg19::chr3:98518647..98518667,-p@chr3:98518647..98518667
-
Hg19::chr3:98530363..98530400,-p@chr3:98530363..98530400
-
Hg19::chr3:98531239..98531265,-p12@DCBLD2
Hg19::chr3:98531283..98531302,-p20@DCBLD2
Hg19::chr3:98536685..98536713,-p8@DCBLD2
Hg19::chr3:98536722..98536741,-p19@DCBLD2


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

No GOStat results

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
multilaminar epithelium9.23e-1583
somite2.27e-1271
presomitic mesoderm2.27e-1271
presumptive segmental plate2.27e-1271
dermomyotome2.27e-1271
trunk paraxial mesoderm2.27e-1271
dense mesenchyme tissue3.25e-1273
skeletal muscle tissue3.62e-1262
striated muscle tissue3.62e-1262
myotome3.62e-1262
paraxial mesoderm5.89e-1272
presumptive paraxial mesoderm5.89e-1272
muscle tissue2.73e-1164
musculature2.73e-1164
musculature of body2.73e-1164
epithelial vesicle2.73e-1178
mesenchyme6.34e-11160
entire embryonic mesenchyme6.34e-11160
trunk mesenchyme7.57e-11122
unilaminar epithelium5.38e-10148
artery1.36e-0942
arterial blood vessel1.36e-0942
arterial system1.36e-0942
organism subdivision1.32e-08264
systemic artery1.52e-0833
systemic arterial system1.52e-0833
trunk4.10e-08199
epithelium6.70e-08306
blood vessel smooth muscle8.76e-0810
arterial system smooth muscle8.76e-0810
artery smooth muscle tissue8.76e-0810
aorta smooth muscle tissue8.76e-0810
cell layer8.90e-08309
pigment epithelium of eye2.01e-0711
female gonad2.45e-0713
smooth muscle tissue6.56e-0715
Disease
Ontology termp-valuen
female reproductive organ cancer4.70e-1027
ovarian cancer8.00e-1014
reproductive organ cancer1.07e-0929


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)
MA0003.12.41061e-07
MA0004.10.193314
MA0006.10.308609
MA0007.10.180248
MA0009.10.580032
MA0014.14.97928e-05
MA0017.10.114723
MA0019.10.824541
MA0024.10.485346
MA0025.12.82051
MA0027.12.15732
MA0028.10.101383
MA0029.10.50258
MA0030.10.492344
MA0031.11.94508
MA0038.10.269828
MA0040.12.18682
MA0041.13.29099
MA0042.10.541224
MA0043.11.41975
MA0046.13.50363
MA0048.10.00932809
MA0050.10.184533
MA0051.10.266537
MA0052.12.19827
MA0055.10.00470761
MA0056.10
MA0057.10.0434899
MA0058.10.12994
MA0059.10.405044
MA0060.10.0387582
MA0061.10.029485
MA0063.10
MA0066.10.270161
MA0067.10.879057
MA0068.10.213016
MA0069.10.566544
MA0070.10.556335
MA0071.11.25272
MA0072.13.42488
MA0073.11.72328e-08
MA0074.10.265952
MA0076.10.139892
MA0077.10.545231
MA0078.10.346453
MA0081.10.405301
MA0083.10.586921
MA0084.11.06048
MA0087.11.35576
MA0088.10.00268743
MA0089.10
MA0090.10.149167
MA0091.10.195166
MA0092.10.168981
MA0093.10.0941737
MA0095.10
MA0098.10
MA0100.10.280715
MA0101.10.0959778
MA0103.10.0875643
MA0105.10.00666152
MA0106.10.302526
MA0107.10.0591705
MA0108.21.10489
MA0109.10
MA0111.10.477838
MA0113.10.315797
MA0114.10.0569149
MA0115.10.805883
MA0116.10.0607301
MA0117.10.614633
MA0119.10.119385
MA0122.10.638621
MA0124.11.8075
MA0125.10.687166
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.11.47785
MA0136.10.27535
MA0139.10.0257123
MA0140.10.238066
MA0141.10.128074
MA0142.11.05085
MA0143.10.315941
MA0144.10.189563
MA0145.10.00353814
MA0146.12.87274e-05
MA0147.10.223797
MA0148.11.7874
MA0149.10.230803
MA0062.20.027823
MA0035.20.237534
MA0039.24.69208e-07
MA0138.20.347473
MA0002.20.0346057
MA0137.20.105044
MA0104.20.151208
MA0047.20.795472
MA0112.20.0591493
MA0065.20.003771
MA0150.10.145358
MA0151.10
MA0152.11.26389
MA0153.10.67139
MA0154.10.0342743
MA0155.10.00260895
MA0156.10.345664
MA0157.11.77115
MA0158.10
MA0159.10.062613
MA0160.10.222325
MA0161.10
MA0162.10.00017322
MA0163.10.000591497
MA0164.10.32594
MA0080.20.31321
MA0018.20.30364
MA0099.20.243305
MA0079.26.21991e-15
MA0102.21.09681
MA0258.11.08978
MA0259.10.0662172
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
SMC3#912653.95919285392970.00685405606151080.029046857693886



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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