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Coexpression cluster:C480: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:24, 17 September 2013


Full id: C480_Pericytes_Skeletal_skeletal_mesenchymal_Hepatic_diaphragm_tongue



Phase1 CAGE Peaks

Hg19::chr11:67186174..67186179,+p@chr11:67186174..67186179
+
Hg19::chr11:67186200..67186211,+p@chr11:67186200..67186211
+
Hg19::chr13:75493774..75493776,-p@chr13:75493774..75493776
-
Hg19::chr18:8054314..8054316,-p@chr18:8054314..8054316
-
Hg19::chr19:48281847..48281853,+p7@SEPW1
Hg19::chr19:48283739..48283754,+p@chr19:48283739..48283754
+
Hg19::chr1:203052309..203052311,-p@chr1:203052309..203052311
-
Hg19::chr1:203055129..203055147,-p1@MYOG
Hg19::chr1:203144944..203144961,-p1@MYBPH
Hg19::chr1:32138785..32138796,-p18@COL16A1
Hg19::chr1:32138798..32138820,-p13@COL16A1
Hg19::chr22:24026194..24026197,-p5@GUSBP11
Hg19::chr2:121637394..121637397,+p@chr2:121637394..121637397
+
Hg19::chr2:218718071..218718103,-p@chr2:218718071..218718103
-
Hg19::chr4:167520111..167520112,-p@chr4:167520111..167520112
-
Hg19::chr8:144874971..144874988,-p@chr8:144874971..144874988
-
Hg19::chr8:144875208..144875222,-p@chr8:144875208..144875222
-
Hg19::chr8:144875233..144875250,-p@chr8:144875233..144875250
-
Hg19::chr8:144875310..144875315,-p19@SCRIB
Hg19::chr9:136390071..136390087,-p1@TMEM8C


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:0005597collagen type XVI0.0169257035205463
GO:0005593FACIT collagen0.0380648999849687
GO:0006942regulation of striated muscle contraction0.0380648999849687
GO:0030934anchoring collagen0.0380648999849687
GO:0032982myosin filament0.044193204806296
GO:0005863striated muscle thick filament0.044193204806296
GO:0005859muscle myosin complex0.044193204806296
GO:0016460myosin II complex0.044193204806296
GO:0006941striated muscle contraction0.044193204806296
GO:0006937regulation of muscle contraction0.044193204806296
GO:0005178integrin binding0.044193204806296
GO:0048741skeletal muscle fiber development0.044193204806296
GO:0048747muscle fiber development0.044193204806296
GO:0008307structural constituent of muscle0.044193204806296
GO:0030017sarcomere0.044193204806296
GO:0008430selenium binding0.044193204806296
GO:0022610biological adhesion0.044193204806296
GO:0007155cell adhesion0.044193204806296
GO:0030016myofibril0.044193204806296
GO:0005581collagen0.044193204806296
GO:0044424intracellular part0.044193204806296
GO:0044449contractile fiber part0.0451849650734512
GO:0043292contractile fiber0.0451849650734512
GO:0005737cytoplasm0.0451849650734512
GO:0007519skeletal muscle development0.0451849650734512



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
skeletal muscle tissue7.27e-2162
striated muscle tissue7.27e-2162
myotome7.27e-2162
muscle tissue3.40e-2064
musculature3.40e-2064
musculature of body3.40e-2064
somite3.83e-1871
presomitic mesoderm3.83e-1871
presumptive segmental plate3.83e-1871
dermomyotome3.83e-1871
trunk paraxial mesoderm3.83e-1871
paraxial mesoderm6.97e-1872
presumptive paraxial mesoderm6.97e-1872
dense mesenchyme tissue1.25e-1773
epithelial vesicle1.85e-1678
multilaminar epithelium1.99e-1583
trunk mesenchyme9.28e-13122
unilaminar epithelium2.28e-10148
throat1.57e-092
mesenchyme1.59e-09160
entire embryonic mesenchyme1.59e-09160
trunk1.78e-07199
musculoskeletal system3.07e-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)
MA0003.10.185667
MA0004.10.533484
MA0006.10.597254
MA0007.10.168078
MA0009.10.561062
MA0014.10.0390946
MA0017.10.342408
MA0019.10.290278
MA0024.10.467291
MA0025.10.684106
MA0027.12.13512
MA0028.10.0924235
MA0029.10.484339
MA0030.10.474212
MA0031.10.41796
MA0038.10.25521
MA0040.10.489524
MA0041.10.193578
MA0042.10.171628
MA0043.10.561349
MA0046.10.551181
MA0048.14.05708
MA0050.10.172223
MA0051.10.251994
MA0052.10.492957
MA0055.10.798134
MA0056.10
MA0057.10.893467
MA0058.11.24845
MA0059.10.760411
MA0060.10.319572
MA0061.10.788088
MA0063.10
MA0066.11.31072
MA0067.10.858361
MA0068.11.68376
MA0069.10.547689
MA0070.10.537571
MA0071.10.22617
MA0072.10.533514
MA0073.16.06187
MA0074.10.251422
MA0076.10.129195
MA0077.11.30604
MA0078.10.33032
MA0081.10.118989
MA0083.10.567893
MA0084.11.03923
MA0087.10.531309
MA0088.13.33863
MA0089.10
MA0090.11.97145
MA0091.11.02897
MA0092.10.157193
MA0093.11.01605
MA0095.10
MA0098.10
MA0100.10.734012
MA0101.10.0872967
MA0103.10.573987
MA0105.11.82388
MA0106.10.28721
MA0107.10.0527035
MA0108.21.06707
MA0109.10
MA0111.10.449411
MA0113.10.300221
MA0114.10.188951
MA0115.10.785493
MA0116.10.44115
MA0117.10.595385
MA0119.10.354175
MA0122.10.619196
MA0124.10.746208
MA0125.10.667416
MA0130.10
MA0131.10.345226
MA0132.10
MA0133.10
MA0135.10.588754
MA0136.10.260607
MA0139.10.0959198
MA0140.10.224213
MA0141.10.755821
MA0142.10.39079
MA0143.10.81259
MA0144.10.0449457
MA0145.10.128234
MA0146.10.497408
MA0147.10.783008
MA0148.10.575245
MA0149.10.21714
MA0062.20.0239298
MA0035.20.223695
MA0039.21.0136
MA0138.20.331323
MA0002.20.542267
MA0137.20.654613
MA0104.20.579321
MA0047.20.277681
MA0112.20.372295
MA0065.21.49681
MA0150.10.418577
MA0151.10
MA0152.10.229055
MA0153.10.65174
MA0154.14.74298
MA0155.11.01632
MA0156.10.0971366
MA0157.10.367703
MA0158.10
MA0159.10.0559104
MA0160.10.601097
MA0161.10
MA0162.10.355774
MA0163.13.14529
MA0164.10.310173
MA0080.20.0856322
MA0018.20.288301
MA0099.20.229319
MA0079.22.78143
MA0102.21.07547
MA0258.10.655463
MA0259.10.469431
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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