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Coexpression cluster:C508: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.318513921657292,

Latest revision as of 11:24, 17 September 2013


Full id: C508_Adipocyte_aorta_smooth_umbilical_bladder_hepatic_penis



Phase1 CAGE Peaks

Hg19::chr10:90695096..90695126,-p@chr10:90695096..90695126
-
Hg19::chr10:90697836..90697854,+p@chr10:90697836..90697854
+
Hg19::chr10:90697845..90697865,-p@chr10:90697845..90697865
-
Hg19::chr10:90697881..90697892,+p@chr10:90697881..90697892
+
Hg19::chr10:90697890..90697903,-p@chr10:90697890..90697903
-
Hg19::chr10:90697895..90697934,+p@chr10:90697895..90697934
+
Hg19::chr10:90697913..90697941,-p@chr10:90697913..90697941
-
Hg19::chr10:90697954..90697970,+p@chr10:90697954..90697970
+
Hg19::chr10:90699296..90699439,-p1@AK127229
Hg19::chr10:90701044..90701054,-p@chr10:90701044..90701054
-
Hg19::chr10:90701565..90701581,-p@chr10:90701565..90701581
-
Hg19::chr10:90701605..90701617,-p@chr10:90701605..90701617
-
Hg19::chr10:90703608..90703675,-p@chr10:90703608..90703675
-
Hg19::chr10:90707015..90707058,+p@chr10:90707015..90707058
+
Hg19::chr10:90707094..90707147,-p@chr10:90707094..90707147
-
Hg19::chr10:90708582..90708630,-p3@ACTA2
Hg19::chr10:90708633..90708655,-p10@ACTA2
Hg19::chr10:90712520..90712536,-p1@ACTA2


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
muscle tissue9.20e-1164
musculature9.20e-1164
musculature of body9.20e-1164
skeletal muscle tissue8.89e-1062
striated muscle tissue8.89e-1062
myotome8.89e-1062
dense mesenchyme tissue3.81e-0973
paraxial mesoderm1.29e-0872
presumptive paraxial mesoderm1.29e-0872
trunk mesenchyme1.51e-08122
somite2.17e-0871
presomitic mesoderm2.17e-0871
presumptive segmental plate2.17e-0871
dermomyotome2.17e-0871
trunk paraxial mesoderm2.17e-0871
mesenchyme4.14e-08160
entire embryonic mesenchyme4.14e-08160
organism subdivision1.73e-07264
trunk5.96e-07199


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)
MA0003.10.000273416
MA0004.10.207008
MA0006.10.101986
MA0007.10.193512
MA0009.13.63588
MA0014.18.02757e-05
MA0017.10.125342
MA0019.10.322194
MA0024.10.50459
MA0025.10.725013
MA0027.14.66151
MA0028.10.111328
MA0029.10.522011
MA0030.10.511665
MA0031.10.454061
MA0038.10.285594
MA0040.10.527306
MA0041.10.220669
MA0042.10.197306
MA0043.10.60049
MA0046.10.590147
MA0048.10.0114521
MA0050.10.197941
MA0051.10.77145
MA0052.10.530811
MA0055.10.02381
MA0056.10
MA0057.10.141662
MA0058.10.141262
MA0059.10.140431
MA0060.10.0444001
MA0061.10.585515
MA0063.10
MA0066.10.285934
MA0067.10.900956
MA0068.10.0222576
MA0069.10.586593
MA0070.10.576293
MA0071.11.30914
MA0072.10.572162
MA0073.14.71255e-08
MA0074.10.281628
MA0076.10.151641
MA0077.10.565087
MA0078.12.56103
MA0081.10.434032
MA0083.10.607144
MA0084.11.08294
MA0087.10.569916
MA0088.10.0658118
MA0089.10
MA0090.10.161293
MA0091.11.13332
MA0092.10.53622
MA0093.10.103729
MA0095.10
MA0098.10
MA0100.10.296726
MA0101.10.700148
MA0103.10.658605
MA0105.10.0429646
MA0106.10.319
MA0107.10.508097
MA0108.20.451357
MA0109.10
MA0111.10.170509
MA0113.10.332535
MA0114.10.228885
MA0115.10.827474
MA0116.10.0681676
MA0117.10.635078
MA0119.10.407815
MA0122.11.58517
MA0124.10.787807
MA0125.10.708116
MA0130.10
MA0131.10.379172
MA0132.10
MA0133.10
MA0135.10.628343
MA0136.10.291242
MA0139.10.0300305
MA0140.16.66628
MA0141.10.139313
MA0142.10.426146
MA0143.10.332682
MA0144.10.0574875
MA0145.10.0260092
MA0146.10.00247058
MA0147.10.0698742
MA0148.10.640121
MA0149.10.245595
MA0062.20.0323736
MA0035.24.61898
MA0039.29.54563e-05
MA0138.21.70306
MA0002.20.999186
MA0137.20.11518
MA0104.20.0440964
MA0047.20.309071
MA0112.20.00394022
MA0065.20.181893
MA0150.11.48153
MA0151.10
MA0152.11.32045
MA0153.10.692238
MA0154.10.0413356
MA0155.10.665536
MA0156.10.116546
MA0157.10.402372
MA0158.10
MA0159.10.0701863
MA0160.10.236884
MA0161.10
MA0162.10.000261548
MA0163.19.54308e-05
MA0164.10.907835
MA0080.20.103778
MA0018.20.320136
MA0099.20.258426
MA0079.24.60127e-10
MA0102.21.11935
MA0258.10.053266
MA0259.10.0740439
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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