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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.577743088126784,

Latest revision as of 11:20, 17 September 2013


Full id: C320_Olfactory_Ewing_smooth_hepatic_Hair_Mesenchymal_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr7:134528663..134528702,+p22@CALD1
Hg19::chr7:134552465..134552517,+p1@CU691860
Hg19::chr7:134613495..134613506,+p45@CALD1
Hg19::chr7:134613535..134613560,+p29@CALD1
Hg19::chr7:134613586..134613622,+p13@CALD1
Hg19::chr7:134617744..134617765,+p18@CALD1
Hg19::chr7:134617784..134617809,+p10@CALD1
Hg19::chr7:134617787..134617804,-p@chr7:134617787..134617804
-
Hg19::chr7:134617811..134617848,+p8@CALD1
Hg19::chr7:134617854..134617915,+p4@CALD1
Hg19::chr7:134617917..134617937,+p17@CALD1
Hg19::chr7:134617937..134617982,-p@chr7:134617937..134617982
-
Hg19::chr7:134617940..134617951,+p32@CALD1
Hg19::chr7:134617957..134617991,+p11@CALD1
Hg19::chr7:134617984..134617989,-p@chr7:134617984..134617989
-
Hg19::chr7:134617990..134618123,-p@chr7:134617990..134618123
-
Hg19::chr7:134617994..134618020,+p20@CALD1
Hg19::chr7:134618090..134618112,+p16@CALD1
Hg19::chr7:134618124..134618144,-p@chr7:134618124..134618144
-
Hg19::chr7:134625860..134625881,+p38@CALD1
Hg19::chr7:134625866..134625911,-p@chr7:134625866..134625911
-
Hg19::chr7:134625911..134625928,+p34@CALD1
Hg19::chr7:134625914..134625938,-p@chr7:134625914..134625938
-
Hg19::chr7:134632290..134632346,+p@chr7:134632290..134632346
+
Hg19::chr7:134632354..134632417,+p@chr7:134632354..134632417
+
Hg19::chr7:134632438..134632530,-p@chr7:134632438..134632530
-
Hg19::chr7:134635150..134635191,-p@chr7:134635150..134635191
-
Hg19::chr7:134644722..134644760,+p44@CALD1
Hg19::chr7:134653144..134653160,+p@chr7:134653144..134653160
+
Hg19::chr7:134653476..134653488,+p@chr7:134653476..134653488
+
Hg19::chr7:134653623..134653707,+p@chr7:134653623..134653707
+
Hg19::chr7:134653818..134653846,+p26@CALD1
Hg19::chr7:134653919..134653969,+p30@CALD1
Hg19::chr7:134654032..134654049,+p39@CALD1
Hg19::chr7:134654089..134654182,+p23@CALD1
Hg19::chr7:134654295..134654363,+p21@CALD1
Hg19::chr7:134654434..134654479,+p36@CALD1


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:0017022myosin binding0.0049452490286118
GO:0005523tropomyosin binding0.00649063935005298
GO:0005516calmodulin binding0.0203991522430237
GO:0006936muscle contraction0.0203991522430237
GO:0003012muscle system process0.0203991522430237
GO:0051674localization of cell0.0338219710349699
GO:0006928cell motility0.0338219710349699
GO:0003779actin binding0.033844048039562
GO:0008092cytoskeletal protein binding0.0414164606146238



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
fibroblast5.53e-1476
non-terminally differentiated cell5.46e-10106
embryonic cell1.95e-08250
muscle precursor cell5.35e-0858
myoblast5.35e-0858
multi-potent skeletal muscle stem cell5.35e-0858
electrically responsive cell1.00e-0761
electrically active cell1.00e-0761
muscle cell1.52e-0755
skin fibroblast2.53e-0723
preadipocyte7.73e-0712
contractile cell9.13e-0759
Uber Anatomy
Ontology termp-valuen
multi-cellular organism8.07e-15656
multi-tissue structure2.00e-12342
anatomical cluster2.03e-11373
anatomical system6.35e-11624
anatomical group1.17e-10625
surface structure1.31e-1099
trunk mesenchyme5.17e-10122
mesenchyme9.35e-10160
entire embryonic mesenchyme9.35e-10160
organism subdivision6.95e-09264
muscle tissue9.95e-0964
musculature9.95e-0964
musculature of body9.95e-0964
multilaminar epithelium1.31e-0883
dense mesenchyme tissue1.43e-0873
paraxial mesoderm3.29e-0872
presumptive paraxial mesoderm3.29e-0872
somite3.44e-0871
presomitic mesoderm3.44e-0871
presumptive segmental plate3.44e-0871
dermomyotome3.44e-0871
trunk paraxial mesoderm3.44e-0871
skeletal muscle tissue4.09e-0862
striated muscle tissue4.09e-0862
myotome4.09e-0862
reproductive structure1.78e-0759
reproductive system1.78e-0759
epithelium1.96e-07306
cell layer2.41e-07309
unilaminar epithelium4.59e-07148
embryonic structure5.36e-07564
trunk8.34e-07199
epithelial vesicle8.70e-0778


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)
MA0003.11.17108e-09
MA0004.10.492707
MA0006.10.017801
MA0007.10.0565706
MA0009.10.348676
MA0014.19.20242e-09
MA0017.10.109976
MA0019.10.133515
MA0024.10.269509
MA0025.10.457382
MA0027.11.8693
MA0028.10.0209428
MA0029.10.283613
MA0030.10.275218
MA0031.10.229546
MA0038.10.354223
MA0040.10.28793
MA0041.10.531519
MA0042.10.465279
MA0043.10.348924
MA0046.10.901813
MA0048.10.00888689
MA0050.111.9484
MA0051.10.107453
MA0052.10.290795
MA0055.10.397462
MA0056.10
MA0057.10.000198151
MA0058.10.894804
MA0059.10.562837
MA0060.10.00361847
MA0061.10.00216489
MA0063.10
MA0066.10.109799
MA0067.10.617744
MA0068.10.000918689
MA0069.10.337164
MA0070.10.328499
MA0071.10.303897
MA0072.10.325036
MA0073.17.51818e-10
MA0074.10.107076
MA0076.10.0367614
MA0077.10.319123
MA0078.10.946517
MA0081.11.28192
MA0083.10.354583
MA0084.10.789341
MA0087.10.863856
MA0088.10.0318075
MA0089.10
MA0090.14.35669
MA0091.10.064608
MA0092.10.421858
MA0093.10.404587
MA0095.10
MA0098.10
MA0100.10.116712
MA0101.10.0190019
MA0103.10.19188
MA0105.10.00114909
MA0106.10.131372
MA0107.10.00792473
MA0108.20.227449
MA0109.10
MA0111.10.0452988
MA0113.10.140523
MA0114.10.00737888
MA0115.10.549953
MA0116.10.0429349
MA0117.10.37852
MA0119.10.0279214
MA0122.10.399455
MA0124.10.513817
MA0125.10.442376
MA0130.10
MA0131.10.173329
MA0132.10
MA0133.10
MA0135.10.372723
MA0136.10.113182
MA0139.10.0383953
MA0140.10.0895621
MA0141.10.0315565
MA0142.11.77078
MA0143.10.140623
MA0144.10.0960756
MA0145.10.0071176
MA0146.13.15322e-09
MA0147.10.125089
MA0148.10.256233
MA0149.10.288466
MA0062.20.00194025
MA0035.20.0892374
MA0039.21.04466e-12
MA0138.20.163015
MA0002.20.05768
MA0137.20.0222989
MA0104.20.0665347
MA0047.20.124773
MA0112.22.7275e-05
MA0065.20.0077811
MA0150.14.28994
MA0151.10
MA0152.10.0926128
MA0153.10.42835
MA0154.10.0392757
MA0155.10.000223711
MA0156.10.0227881
MA0157.10.55667
MA0158.10
MA0159.10.0087896
MA0160.10.0801079
MA0161.10
MA0162.11.04268e-07
MA0163.11.31301e-08
MA0164.12.74569
MA0080.20.0183872
MA0018.20.132133
MA0099.20.0927801
MA0079.22.97977e-14
MA0102.20.824164
MA0258.10.00516272
MA0259.10.0489563
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

No analysis results for this cluster

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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