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{{Coexpression_clusters
{
|full_id=C1080_Fibroblast_mesenchymal_neuroectodermal_Hair_Mesenchymal_Smooth_alveolar

Latest revision as of 11:37, 17 September 2013


Full id: C1080_Fibroblast_mesenchymal_neuroectodermal_Hair_Mesenchymal_Smooth_alveolar



Phase1 CAGE Peaks

Hg19::chr3:55521323..55521342,-p5@WNT5A
Hg19::chr3:55521350..55521362,-p17@WNT5A
Hg19::chr3:55521543..55521588,-p7@WNT5A
Hg19::chr3:55521611..55521652,-p8@WNT5A
Hg19::chr3:55521660..55521688,-p11@WNT5A
Hg19::chr3:55522284..55522331,-p@chr3:55522284..55522331
-
Hg19::chr3:55522429..55522447,-p@chr3:55522429..55522447
-
Hg19::chr3:55522502..55522553,-p@chr3:55522502..55522553
-


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>

Cell Type
Ontology termp-valuen
fibroblast2.10e-1476
non-terminally differentiated cell9.48e-10106
muscle precursor cell1.92e-0858
myoblast1.92e-0858
multi-potent skeletal muscle stem cell1.92e-0858
skin fibroblast6.46e-0823
extraembryonic cell6.90e-0819
muscle cell2.13e-0755
contractile cell2.48e-0759
Uber Anatomy
Ontology termp-valuen
multi-cellular organism2.14e-12656
surface structure8.89e-1299
anatomical system4.73e-10624
anatomical group6.30e-10625
multilaminar epithelium1.06e-0983
multi-tissue structure1.41e-09342
dense mesenchyme tissue6.30e-0973
somite7.35e-0971
presomitic mesoderm7.35e-0971
presumptive segmental plate7.35e-0971
dermomyotome7.35e-0971
trunk paraxial mesoderm7.35e-0971
paraxial mesoderm1.49e-0872
presumptive paraxial mesoderm1.49e-0872
organ component layer3.76e-0866
integument4.83e-0846
integumental system4.83e-0846
epithelial vesicle6.27e-0878
extraembryonic structure6.59e-0824
skeletal muscle tissue1.30e-0762
striated muscle tissue1.30e-0762
myotome1.30e-0762
organism subdivision1.56e-07264
embryonic structure1.70e-07564
muscle tissue1.85e-0764
musculature1.85e-0764
musculature of body1.85e-0764
germ layer4.37e-07560
germ layer / neural crest4.37e-07560
embryonic tissue4.37e-07560
presumptive structure4.37e-07560
germ layer / neural crest derived structure4.37e-07560
epiblast (generic)4.37e-07560
skin of body5.96e-0741
embryo5.98e-07592
extraembryonic membrane6.60e-0714
membranous layer6.60e-0714
Disease
Ontology termp-valuen
ovarian cancer8.21e-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)
MA0003.10.248189
MA0004.10.455723
MA0006.10.812175
MA0007.10.437331
MA0009.10.918715
MA0014.10.134069
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.316923
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.11.64271
MA0056.10
MA0057.12.14064
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.12.60013
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.16.51901
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.12.13567
MA0084.11.42483
MA0087.10.885691
MA0088.10.199853
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.11.07975
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.11.40058
MA0101.10.30624
MA0103.10.792149
MA0105.10.279181
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.0613434
MA0146.10.0399277
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.0817047
MA0138.21.57302
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.0572179
MA0065.20.844872
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.625961
MA0163.10.75401
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.25.96581
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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
CTCF#1066485.360256373075031.46631949289063e-065.66559162108785e-05
GTF2F1#296257.962288047973530.0001362053831339150.0017808154743519
POLR2A#543082.147453176558070.002210725788971910.012723094212511
TBP#690883.706770687096392.80450451364125e-050.000592194999798176



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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