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{{Coexpression_clusters
{
|full_id=C851_Fibroblast_mesenchymal_Myoblast_normal_Olfactory_skeletal_Osteoblast

Latest revision as of 11:32, 17 September 2013


Full id: C851_Fibroblast_mesenchymal_Myoblast_normal_Olfactory_skeletal_Osteoblast



Phase1 CAGE Peaks

Hg19::chr1:170632867..170632878,+p21@PRRX1
Hg19::chr1:170632907..170632916,+p22@PRRX1
Hg19::chr1:170632959..170632987,+p4@PRRX1
Hg19::chr1:170633225..170633230,+p25@PRRX1
Hg19::chr1:170633245..170633256,+p14@PRRX1
Hg19::chr1:170633262..170633285,+p3@PRRX1
Hg19::chr1:170633294..170633303,+p23@PRRX1
Hg19::chr1:170633348..170633399,+p2@PRRX1
Hg19::chr1:170633410..170633422,+p2@M95929
Hg19::chr1:170633459..170633473,+p1@M95929


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><br>

Uber Anatomy
Ontology termp-valuen
dense mesenchyme tissue1.01e-2773
paraxial mesoderm5.69e-2772
presumptive paraxial mesoderm5.69e-2772
somite7.64e-2771
presomitic mesoderm7.64e-2771
presumptive segmental plate7.64e-2771
dermomyotome7.64e-2771
trunk paraxial mesoderm7.64e-2771
epithelial vesicle8.18e-2278
multilaminar epithelium8.26e-2283
muscle tissue1.24e-2164
musculature1.24e-2164
musculature of body1.24e-2164
skeletal muscle tissue1.34e-2162
striated muscle tissue1.34e-2162
myotome1.34e-2162
structure with developmental contribution from neural crest5.72e-14132
surface structure2.71e-1299
multi-tissue structure3.41e-12342
tissue5.18e-12773
trunk mesenchyme8.12e-12122
mesenchyme2.80e-11160
entire embryonic mesenchyme2.80e-11160
primary circulatory organ3.94e-1027
integument5.52e-1046
integumental system5.52e-1046
splanchnic layer of lateral plate mesoderm8.86e-1083
heart1.22e-0924
primitive heart tube1.22e-0924
primary heart field1.22e-0924
anterior lateral plate mesoderm1.22e-0924
heart tube1.22e-0924
heart primordium1.22e-0924
cardiac mesoderm1.22e-0924
cardiogenic plate1.22e-0924
heart rudiment1.22e-0924
adult organism1.80e-09114
multi-cellular organism2.03e-09656
cell layer5.04e-09309
skin of body7.72e-0941
organism subdivision7.77e-09264
artery1.00e-0842
arterial blood vessel1.00e-0842
arterial system1.00e-0842
epithelium2.65e-08306
systemic artery2.88e-0833
systemic arterial system2.88e-0833
blood vessel smooth muscle5.10e-0710
arterial system smooth muscle5.10e-0710
artery smooth muscle tissue5.10e-0710
aorta smooth muscle tissue5.10e-0710
anatomical system5.19e-07624
anatomical group6.88e-07625
smooth muscle tissue9.04e-0715
dermis9.40e-079
dermatome9.40e-079
future dermis9.40e-079


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)
MA0003.10.000221536
MA0004.10.380329
MA0006.10.665232
MA0007.10.363007
MA0009.10.828613
MA0014.10.0679667
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.368721
MA0051.11.19169
MA0052.12.97852
MA0055.10.344701
MA0056.10
MA0057.12.85487
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.757837
MA0063.10
MA0066.14.18732
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.16.58431
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.13.06606
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.126492
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.228129
MA0105.15.44218
MA0106.11.28468
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.109245
MA0140.11.11568
MA0141.11.43869
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.602634
MA0146.10.0169564
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.713007
MA0138.20.569505
MA0002.20.80943
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.20.904106
MA0065.20.147044
MA0150.10.315136
MA0151.10
MA0152.11.97388
MA0153.10.926242
MA0154.10.0494985
MA0155.10.030416
MA0156.11.31919
MA0157.10.612166
MA0158.10
MA0159.10.544949
MA0160.10.417847
MA0161.10
MA0162.10.229496
MA0163.13.43241
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.20.875426
MA0102.21.36707
MA0258.12.11165
MA0259.10.560522
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
EP300#203374.741759208356240.0001211445349442930.00164186531080288
SUZ12#23512315.03473427331890.0008575295983126410.00645427599583265



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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