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Coexpression cluster:C396: Difference between revisions

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{{Coexpression_clusters
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|full_id=C396_Mesenchymal_Chondrocyte_Smooth_Preadipocyte_Placental_Fibroblast_Hepatic
|id=C396
}}

Latest revision as of 11:22, 17 September 2013


Full id: C396_Mesenchymal_Chondrocyte_Smooth_Preadipocyte_Placental_Fibroblast_Hepatic



Phase1 CAGE Peaks

Hg19::chr9:137533615..137533660,+p1@COL5A1
Hg19::chr9:137533678..137533693,+p2@COL5A1
Hg19::chr9:137582780..137582797,+p11@COL5A1
Hg19::chr9:137582822..137582849,+p8@COL5A1
Hg19::chr9:137582854..137582895,+p7@COL5A1
Hg19::chr9:137591763..137591784,+p@chr9:137591763..137591784
+
Hg19::chr9:137591792..137591823,+p@chr9:137591792..137591823
+
Hg19::chr9:137591859..137591883,+p@chr9:137591859..137591883
+
Hg19::chr9:137591918..137591938,+p@chr9:137591918..137591938
+
Hg19::chr9:137593007..137593032,+p@chr9:137593007..137593032
+
Hg19::chr9:137619101..137619121,+p@chr9:137619101..137619121
+
Hg19::chr9:137619145..137619163,+p@chr9:137619145..137619163
+
Hg19::chr9:137620521..137620564,+p@chr9:137620521..137620564
+
Hg19::chr9:137620548..137620598,-p@chr9:137620548..137620598
-
Hg19::chr9:137620587..137620603,+p@chr9:137620587..137620603
+
Hg19::chr9:137622077..137622092,+p@chr9:137622077..137622092
+
Hg19::chr9:137622160..137622173,+p@chr9:137622160..137622173
+
Hg19::chr9:137622234..137622248,+p@chr9:137622234..137622248
+
Hg19::chr9:137622273..137622284,+p@chr9:137622273..137622284
+
Hg19::chr9:137717707..137717723,+p@chr9:137717707..137717723
+
Hg19::chr9:137726871..137726892,+p@chr9:137726871..137726892
+
Hg19::chr9:137734427..137734440,+p10@COL5A1
Hg19::chr9:137734487..137734510,+p5@COL5A1
Hg19::chr9:137734628..137734645,+p20@COL5A1
Hg19::chr9:137734900..137734994,+p4@COL5A1
Hg19::chr9:137735438..137735469,+p13@COL5A1
Hg19::chr9:137735933..137735964,+p@chr9:137735933..137735964
+


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 tissue4.17e-1464
musculature4.17e-1464
musculature of body4.17e-1464
skeletal muscle tissue5.19e-1462
striated muscle tissue5.19e-1462
myotome5.19e-1462
dense mesenchyme tissue1.90e-1173
somite2.67e-1171
presomitic mesoderm2.67e-1171
presumptive segmental plate2.67e-1171
dermomyotome2.67e-1171
trunk paraxial mesoderm2.67e-1171
paraxial mesoderm6.70e-1172
presumptive paraxial mesoderm6.70e-1172
extraembryonic structure8.25e-1124
epithelial vesicle2.98e-1078
splanchnic layer of lateral plate mesoderm8.95e-1083
extraembryonic membrane3.37e-0914
membranous layer3.37e-0914
multilaminar epithelium5.98e-0983
trunk mesenchyme2.14e-08122
mesenchyme1.89e-07160
entire embryonic mesenchyme1.89e-07160
mesoderm6.63e-07315
mesoderm-derived structure6.63e-07315
presumptive mesoderm6.63e-07315
artery7.60e-0742
arterial blood vessel7.60e-0742
arterial system7.60e-0742


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)
MA0003.10.316498
MA0004.10.115462
MA0006.10.677636
MA0007.11.69378
MA0009.10.45361
MA0014.10.131286
MA0017.10.211842
MA0019.10.206961
MA0024.10.366071
MA0025.10.570597
MA0027.12.00534
MA0028.11.12043
MA0029.10.381857
MA0030.10.372472
MA0031.10.320773
MA0038.10.176878
MA0040.10.38667
MA0041.10.125771
MA0042.10.108251
MA0043.10.453881
MA0046.10.444311
MA0048.10.331187
MA0050.10.108721
MA0051.10.174152
MA0052.10.389861
MA0055.10.47967
MA0056.10
MA0057.10.479002
MA0058.10.242246
MA0059.10.884777
MA0060.10.168418
MA0061.11.01051
MA0063.10
MA0066.10.524799
MA0067.10.739032
MA0068.10.182546
MA0069.10.441028
MA0070.16.22243
MA0071.10.905737
MA0072.10.427724
MA0073.10.548045
MA0074.10.993196
MA0076.10.943104
MA0077.10.421218
MA0078.10.242013
MA0081.10.517137
MA0083.10.460049
MA0084.10.916043
MA0087.10.425657
MA0088.10.138004
MA0089.10
MA0090.10.280795
MA0091.10.373385
MA0092.10.0969694
MA0093.10.0447606
MA0095.10
MA0098.10
MA0100.10.185942
MA0101.10.697835
MA0103.10.361926
MA0105.11.0951
MA0106.10.204305
MA0107.10.762369
MA0108.20.318371
MA0109.10
MA0111.10.620854
MA0113.10.2156
MA0114.11.08668
MA0115.10.668285
MA0116.10.257586
MA0117.11.2196
MA0119.10.481029
MA0122.10.50863
MA0124.10.630319
MA0125.10.554615
MA0130.10
MA0131.12.82448
MA0132.10
MA0133.10
MA0135.10.479757
MA0136.10.181467
MA0139.10.932211
MA0140.10.150858
MA0141.11.83914
MA0142.10.296096
MA0143.10.215723
MA0144.10.217815
MA0145.10.601271
MA0146.10.0959237
MA0147.12.03882
MA0148.10.806841
MA0149.10.874165
MA0062.21.31678
MA0035.20.150428
MA0039.21.03541
MA0138.21.26338
MA0002.22.84818
MA0137.20.192569
MA0104.22.00069
MA0047.20.196083
MA0112.20.25238
MA0065.20.290245
MA0150.10.575473
MA0151.10
MA0152.10.47
MA0153.10.539635
MA0154.10.144416
MA0155.12.10059
MA0156.10.195153
MA0157.10.275302
MA0158.10
MA0159.10.793879
MA0160.10.428183
MA0161.10
MA0162.10.255958
MA0163.10.0922192
MA0164.10.224291
MA0080.20.171095
MA0018.20.592438
MA0099.20.155103
MA0079.20.488265
MA0102.20.951693
MA0258.10.391387
MA0259.11.62724
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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