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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=1.09648090175757,0.

Latest revision as of 14:18, 17 September 2013


Full id: C4699_Mesenchymal_Urothelial_vagina_Renal_MCF7_salivary_skeletal



Phase1 CAGE Peaks

Hg19::chr7:75931982..75932005,+p1@HSPB1
Hg19::chr7:75932326..75932393,-p@chr7:75932326..75932393
-
Hg19::chrX:49090623..49090648,-p2@HSPB1P2


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:0006446regulation of translational initiation0.0362062875309078
GO:0006986response to unfolded protein0.0362062875309078
GO:0051789response to protein stimulus0.0362062875309078
GO:0006413translational initiation0.0362062875309078
GO:0022618protein-RNA complex assembly0.0362062875309078
GO:0009986cell surface0.0362062875309078
GO:0006916anti-apoptosis0.0362062875309078
GO:0006417regulation of translation0.0362062875309078
GO:0031326regulation of cellular biosynthetic process0.0362062875309078
GO:0009889regulation of biosynthetic process0.0362062875309078
GO:0043066negative regulation of apoptosis0.0362062875309078
GO:0043069negative regulation of programmed cell death0.0362062875309078
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0362062875309078
GO:0009607response to biotic stimulus0.0394968125010513
GO:0051674localization of cell0.0458005857765218
GO:0006928cell motility0.0458005857765218
GO:0051246regulation of protein metabolic process0.0474958616438451



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>

Cell Type
Ontology termp-valuen
embryonic cell3.30e-14250
mesodermal cell8.54e-13121
epithelial cell2.30e-08253
endothelial cell4.72e-0836
endothelial cell of vascular tree6.71e-0824
contractile cell1.90e-0759
lining cell2.43e-0758
barrier cell2.43e-0758
muscle precursor cell2.59e-0758
myoblast2.59e-0758
multi-potent skeletal muscle stem cell2.59e-0758
muscle cell7.88e-0755
meso-epithelial cell9.93e-0745
Uber Anatomy
Ontology termp-valuen
organism subdivision4.25e-18264
trunk3.20e-15199
multi-cellular organism7.11e-15656
splanchnic layer of lateral plate mesoderm8.98e-1583
vessel1.73e-1368
vasculature8.30e-1378
vascular system8.30e-1378
trunk mesenchyme8.66e-13122
epithelial tube2.74e-12117
epithelial tube open at both ends3.08e-1259
blood vessel3.08e-1259
blood vasculature3.08e-1259
vascular cord3.08e-1259
unilaminar epithelium5.31e-12148
mesenchyme8.93e-12160
entire embryonic mesenchyme8.93e-12160
epithelial vesicle3.00e-1178
multi-tissue structure7.42e-11342
multilaminar epithelium1.19e-1083
anatomical system5.42e-10624
epithelium5.48e-10306
surface structure7.39e-1099
anatomical group7.64e-10625
cell layer1.31e-09309
anatomical cluster1.46e-09373
muscle tissue2.37e-0964
musculature2.37e-0964
musculature of body2.37e-0964
somite2.57e-0971
presomitic mesoderm2.57e-0971
presumptive segmental plate2.57e-0971
dermomyotome2.57e-0971
trunk paraxial mesoderm2.57e-0971
dense mesenchyme tissue2.72e-0973
paraxial mesoderm3.61e-0972
presumptive paraxial mesoderm3.61e-0972
skeletal muscle tissue4.58e-0962
striated muscle tissue4.58e-0962
myotome4.58e-0962
anatomical conduit5.29e-09240
circulatory system5.43e-09112
subdivision of trunk9.51e-09112
cardiovascular system5.41e-08109
compound organ7.49e-0868
endoderm-derived structure1.36e-07160
endoderm1.36e-07160
presumptive endoderm1.36e-07160
artery1.47e-0742
arterial blood vessel1.47e-0742
arterial system1.47e-0742
simple squamous epithelium6.19e-0722
developing anatomical structure6.97e-07581
squamous epithelium7.18e-0725
renal system7.22e-0748
embryonic structure8.29e-07564


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.13.37768
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.11.66081
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
NR3C1#290829.982015554115360.01278474365547170.0460804059440161



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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