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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:47, 17 September 2013


Full id: C1542_Fibroblast_ductal_liposarcoma_large_normal_mesenchymal_Myoblast



Phase1 CAGE Peaks

Hg19::chr8:18942243..18942259,-p8@PSD3
Hg19::chr8:18942279..18942294,-p11@PSD3
Hg19::chr8:18942296..18942344,-p6@PSD3
Hg19::chr8:18942386..18942401,-p22@PSD3
Hg19::chr8:18942407..18942448,-p14@PSD3
Hg19::chr8:18942514..18942527,-p24@PSD3


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>

Cell Type
Ontology termp-valuen
fibroblast4.06e-2576
skin fibroblast9.82e-1623
multi fate stem cell2.47e-14427
somatic stem cell2.25e-13433
stem cell3.69e-12441
muscle precursor cell4.35e-1158
myoblast4.35e-1158
multi-potent skeletal muscle stem cell4.35e-1158
non-terminally differentiated cell1.01e-10106
muscle cell2.52e-0955
connective tissue cell8.29e-09361
contractile cell2.15e-0859
somatic cell7.29e-08588
mesenchymal cell1.26e-07354
motile cell1.96e-07386
stromal cell2.29e-0728
electrically responsive cell2.92e-0761
electrically active cell2.92e-0761
Uber Anatomy
Ontology termp-valuen
dense mesenchyme tissue2.21e-1473
somite2.46e-1471
presomitic mesoderm2.46e-1471
presumptive segmental plate2.46e-1471
dermomyotome2.46e-1471
trunk paraxial mesoderm2.46e-1471
paraxial mesoderm6.95e-1472
presumptive paraxial mesoderm6.95e-1472
mesenchyme1.30e-13160
entire embryonic mesenchyme1.30e-13160
epithelial vesicle5.10e-1278
multilaminar epithelium2.34e-1183
muscle tissue2.21e-1064
musculature2.21e-1064
musculature of body2.21e-1064
integument3.25e-1046
integumental system3.25e-1046
connective tissue3.64e-10371
skeletal muscle tissue5.18e-1062
striated muscle tissue5.18e-1062
myotome5.18e-1062
skin of body5.39e-1041
trunk mesenchyme1.14e-09122
tissue1.88e-09773
surface structure3.05e-0999
multi-tissue structure4.94e-08342
dermis5.56e-079
dermatome5.56e-079
future dermis5.56e-079
musculoskeletal system8.89e-07167


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)
MA0003.10.176622
MA0004.10.558729
MA0006.10.391183
MA0007.12.2901
MA0009.11.03681
MA0014.10.108006
MA0017.11.935
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.111.3353
MA0050.11.34656
MA0051.10.661179
MA0052.12.20326
MA0055.120.3769
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.11.09642
MA0069.15.4158
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00076337
MA0074.10.660398
MA0076.10.475586
MA0077.12.28163
MA0078.10.763954
MA0081.12.02016
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.61871
MA0089.10
MA0090.12.13027
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.15.46746
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.11.52717
MA0115.11.28169
MA0116.18.73044
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.12.72169
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.11.16614
MA0146.11.8938
MA0147.10.327615
MA0148.10.584698
MA0149.13.68937
MA0062.20.23336
MA0035.20.621793
MA0039.20.35955
MA0138.21.80506
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.22.25875
MA0065.20.354331
MA0150.14.22814
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.110.7678
MA0155.10.0961854
MA0156.11.07131
MA0157.10.810597
MA0158.10
MA0159.13.2961
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.508943
MA0164.10.738243
MA0080.22.70673
MA0018.20.709805
MA0099.22.58359
MA0079.20.248693
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
FOS#235368.99795530889441.88302066097805e-066.94914469299952e-05
GATA2#2624612.7449317335542.33109997620343e-071.22772440955476e-05
POLR2A#543062.147453176558070.01019570676818780.0380772186362513



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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