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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:35, 17 September 2013


Full id: C1002_Mesenchymal_Whole_Smooth_Renal_osteosarcoma_Fibroblast_Reticulocytes



Phase1 CAGE Peaks

Hg19::chr11:66367106..66367110,+p4@CCS
Hg19::chr12:49717819..49717823,+p@chr12:49717819..49717823
+
Hg19::chr17:5284799..5284803,+p@chr17:5284799..5284803
+
Hg19::chr1:149897719..149897733,-p@chr1:149897719..149897733
-
Hg19::chr1:156223236..156223240,-p4@SMG5
Hg19::chr1:45471462..45471466,-p2@HECTD3
Hg19::chr20:44586221..44586225,-p@chr20:44586221..44586225
-
Hg19::chr20:44983518..44983521,-p@chr20:44983518..44983521
-


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:0015680intracellular copper ion transport0.0112151183327446
GO:0051721protein phosphatase 2A binding0.0129779004996243
GO:0051353positive regulation of oxidoreductase activity0.0129779004996243
GO:0035303regulation of dephosphorylation0.0129779004996243
GO:0004785copper, zinc superoxide dismutase activity0.0129779004996243
GO:0016721oxidoreductase activity, acting on superoxide radicals as acceptor0.0129779004996243
GO:0004784superoxide dismutase activity0.0129779004996243
GO:0030071regulation of mitotic metaphase/anaphase transition0.0129779004996243
GO:0007091mitotic metaphase/anaphase transition0.0129779004996243
GO:0051341regulation of oxidoreductase activity0.0129779004996243
GO:0005375copper ion transmembrane transporter activity0.0129779004996243
GO:0019903protein phosphatase binding0.0129779004996243
GO:0005680anaphase-promoting complex0.0129779004996243
GO:0006825copper ion transport0.0129779004996243
GO:0006801superoxide metabolic process0.0129779004996243
GO:0000184mRNA catabolic process, nonsense-mediated decay0.0129779004996243
GO:0000152nuclear ubiquitin ligase complex0.0129779004996243
GO:0006406mRNA export from nucleus0.0129779004996243
GO:0019902phosphatase binding0.0129779004996243
GO:0046907intracellular transport0.0134110274761918
GO:0006402mRNA catabolic process0.0146159308186139
GO:0046915transition metal ion transmembrane transporter activity0.0146159308186139
GO:0006405RNA export from nucleus0.0146159308186139
GO:0051649establishment of cellular localization0.0162125008845377
GO:0051641cellular localization0.0163590933226291
GO:0051168nuclear export0.0184004411671435
GO:0006800oxygen and reactive oxygen species metabolic process0.0184004411671435
GO:0006401RNA catabolic process0.0184004411671435
GO:0015082di-, tri-valent inorganic cation transmembrane transporter activity0.020850759210351
GO:0005634nucleus0.0234028841151839
GO:0007088regulation of mitosis0.0234028841151839
GO:0051174regulation of phosphorus metabolic process0.0234028841151839
GO:0019220regulation of phosphate metabolic process0.0234028841151839
GO:0051028mRNA transport0.0257257353024162
GO:0000151ubiquitin ligase complex0.0257257353024162
GO:0065007biological regulation0.0257257353024162
GO:0050658RNA transport0.0257257353024162
GO:0051236establishment of RNA localization0.0257257353024162
GO:0050657nucleic acid transport0.0257257353024162
GO:0006403RNA localization0.0257257353024162
GO:0000041transition metal ion transport0.027686652566795
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.027686652566795
GO:0005507copper ion binding0.0304114713492289
GO:0006913nucleocytoplasmic transport0.0387019507964772
GO:0051169nuclear transport0.0387019507964772
GO:0004842ubiquitin-protein ligase activity0.0394187598909581
GO:0008639small protein conjugating enzyme activity0.0394187598909581
GO:0043231intracellular membrane-bound organelle0.0454542410847666
GO:0043227membrane-bound organelle0.0454542410847666
GO:0005515protein binding0.0472949942100303



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
native cell3.06e-11722
contractile cell4.95e-0859
animal cell1.01e-07679
eukaryotic cell1.01e-07679
muscle precursor cell3.31e-0758
myoblast3.31e-0758
multi-potent skeletal muscle stem cell3.31e-0758
somatic cell3.43e-07588
non-terminally differentiated cell4.27e-07106
Uber Anatomy
Ontology termp-valuen
unilaminar epithelium4.78e-10148
cardiovascular system3.27e-09109
circulatory system2.02e-08112
multilaminar epithelium2.24e-0883
organism subdivision1.14e-07264
blood1.81e-0715
haemolymphatic fluid1.81e-0715
organism substance1.81e-0715
epithelial vesicle4.67e-0778
somite5.61e-0771
presomitic mesoderm5.61e-0771
presumptive segmental plate5.61e-0771
dermomyotome5.61e-0771
trunk paraxial mesoderm5.61e-0771


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)
MA0003.10.06829
MA0004.10.455723
MA0006.10.300178
MA0007.11.1148
MA0009.12.12026
MA0014.10.134069
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.118169
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.948176
MA0060.10.190336
MA0061.10.961853
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.11.33409
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.0344109
MA0074.11.36092
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.948525
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.441522
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.792149
MA0105.10.586268
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.11.04489
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.11.25157
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.944441
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.11.7555
MA0146.10.418694
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.164269
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.79629
MA0065.20.226158
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.577214
MA0155.10.764865
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.0517199
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.00818581
MA0102.21.46209
MA0258.11.13653
MA0259.10.699589
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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