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

Latest revision as of 11:21, 17 September 2013


Full id: C356_renal_Smooth_Chondrocyte_thyroid_serous_Small_mesenchymal



Phase1 CAGE Peaks

Hg19::chr10:102106384..102106429,+p15@SCD
Hg19::chr10:75532821..75532859,+p@chr10:75532821..75532859
+
Hg19::chr12:105286070..105286074,-p@chr12:105286070..105286074
-
Hg19::chr12:125398498..125398506,-p16@UBC
Hg19::chr12:125398630..125398643,-p4@UBC
Hg19::chr19:41882466..41882478,+p9@TMEM91
Hg19::chr19:41882598..41882689,+p3@TMEM91
Hg19::chr1:16353510..16353514,+p@chr1:16353510..16353514
+
Hg19::chr21:35445827..35445886,+p1@MRPS6
p1@SLC5A3
Hg19::chr21:35452404..35452441,+p@chr21:35452404..35452441
+
Hg19::chr21:35454368..35454370,+p@chr21:35454368..35454370
+
Hg19::chr21:35470304..35470310,+p@chr21:35470304..35470310
+
Hg19::chr21:35484158..35484164,+p@chr21:35484158..35484164
+
Hg19::chr21:35495858..35495862,+p4@MRPS6
Hg19::chr21:35496814..35496818,+p@chr21:35496814..35496818
+
Hg19::chr21:41029235..41029269,+p2@B3GALT5
Hg19::chr2:70780951..70780966,-p1@TGFA
Hg19::chr2:70781087..70781098,-p2@TGFA
Hg19::chr4:188508175..188508193,-p@chr4:188508175..188508193
-
Hg19::chr5:159659030..159659074,+p3@FABP6
Hg19::chr6:15526561..15526569,+p@chr6:15526561..15526569
+
Hg19::chr6:43737939..43737956,+p1@VEGFA
Hg19::chr6:43745444..43745451,+p13@VEGFA
Hg19::chr6:43745909..43745939,+p15@VEGFA
Hg19::chr6:43746193..43746214,+p6@VEGFA
Hg19::chr6:43752516..43752532,+p4@VEGFA
Hg19::chr6:43753591..43753612,+p@chr6:43753591..43753612
+
Hg19::chr7:125078119..125078156,+p2@ENST00000458437
Hg19::chr7:47579188..47579231,-p13@TNS3
Hg19::chr8:134250145..134250165,-p13@NDRG1
Hg19::chr8:25337575..25337596,+p@chr8:25337575..25337596
+


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

p.valueFDRnGenesnPathwayName
1.74727516305728e-060.00110602517821526371PPAR signaling pathway (KEGG):03320



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:0042127regulation of cell proliferation0.0151338388640772
GO:0001525angiogenesis0.0151338388640772
GO:0048514blood vessel morphogenesis0.0151338388640772
GO:0008283cell proliferation0.0151338388640772
GO:0048646anatomical structure formation0.0151338388640772
GO:0009967positive regulation of signal transduction0.0151338388640772
GO:0001568blood vessel development0.0151338388640772
GO:0001944vasculature development0.0151338388640772
GO:0005155epidermal growth factor receptor activating ligand activity0.0151338388640772
GO:0050840extracellular matrix binding0.0151338388640772
GO:0005172vascular endothelial growth factor receptor binding0.0151338388640772
GO:0045741positive regulation of epidermal growth factor receptor activity0.0151338388640772
GO:0004768stearoyl-CoA 9-desaturase activity0.0151338388640772
GO:0030949positive regulation of vascular endothelial growth factor receptor signaling pathway0.0151338388640772
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0155861889547463
GO:0030947regulation of vascular endothelial growth factor receptor signaling pathway0.0165509309304655
GO:0008284positive regulation of cell proliferation0.0168920544335655
GO:0001948glycoprotein binding0.0176415992128267
GO:0008083growth factor activity0.0176415992128267
GO:0008499UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity0.0176415992128267
GO:0045742positive regulation of epidermal growth factor receptor signaling pathway0.0176415992128267
GO:0050930induction of positive chemotaxis0.0176415992128267
GO:0007176regulation of epidermal growth factor receptor activity0.0176415992128267
GO:0007167enzyme linked receptor protein signaling pathway0.0176415992128267
GO:0005154epidermal growth factor receptor binding0.0176415992128267
GO:0048531beta-1,3-galactosyltransferase activity0.0176415992128267
GO:0050926regulation of positive chemotaxis0.0176415992128267
GO:0050927positive regulation of positive chemotaxis0.0176415992128267
GO:0050918positive chemotaxis0.0176415992128267
GO:0004708MAP kinase kinase activity0.0176415992128267
GO:0048010vascular endothelial growth factor receptor signaling pathway0.0176415992128267
GO:0004712protein serine/threonine/tyrosine kinase activity0.0176415992128267
GO:0050921positive regulation of chemotaxis0.0176415992128267
GO:0050920regulation of chemotaxis0.0176415992128267
GO:0016717oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water0.0176415992128267
GO:0045840positive regulation of mitosis0.0176415992128267
GO:0009887organ morphogenesis0.0181039866972444
GO:0042058regulation of epidermal growth factor receptor signaling pathway0.0181039866972444
GO:0035250UDP-galactosyltransferase activity0.0230579040204921
GO:0050679positive regulation of epithelial cell proliferation0.023220920115621
GO:0001570vasculogenesis0.023220920115621
GO:0045787positive regulation of progression through cell cycle0.0302053811995919
GO:0031177phosphopantetheine binding0.0324452868894586
GO:0005615extracellular space0.0324452868894586
GO:0050678regulation of epithelial cell proliferation0.035217840976197
GO:0005504fatty acid binding0.035596977264209
GO:0007173epidermal growth factor receptor signaling pathway0.0360018094262514
GO:0050673epithelial cell proliferation0.0360018094262514
GO:0042221response to chemical stimulus0.0360018094262514
GO:0010038response to metal ion0.0369596962407415
GO:0016020membrane0.039237620499413
GO:0008378galactosyltransferase activity0.0405941435874171
GO:0010035response to inorganic substance0.0418110153633352
GO:0001666response to hypoxia0.0468701625904609



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><br><br><br>


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)
MA0003.10.187444
MA0004.10.0905471
MA0006.10.296883
MA0007.10.586462
MA0009.10.406485
MA0014.11.1246
MA0017.10.0420572
MA0019.10.989855
MA0024.10.322368
MA0025.10.520106
MA0027.11.94566
MA0028.10.139739
MA0029.10.337465
MA0030.10.328486
MA0031.10.279263
MA0038.10.145356
MA0040.10.342075
MA0041.10.0995936
MA0042.10.285998
MA0043.11.04839
MA0046.11.02822
MA0048.10.124274
MA0050.10.0846723
MA0051.10.142882
MA0052.10.345132
MA0055.19.8929e-06
MA0056.10
MA0057.10.20555
MA0058.10.0506385
MA0059.10.187652
MA0060.10.041198
MA0061.11.08604
MA0063.10
MA0066.10.145606
MA0067.10.685278
MA0068.10.821915
MA0069.10.394339
MA0070.10.385179
MA0071.10.123343
MA0072.10.381514
MA0073.14.89331
MA0074.10.438848
MA0076.10.0564857
MA0077.10.37525
MA0078.10.205266
MA0081.10.0502365
MA0083.10.412707
MA0084.10.860109
MA0087.10.379524
MA0088.10.14141
MA0089.10
MA0090.10.223118
MA0091.10.306639
MA0092.10.258792
MA0093.10.127599
MA0095.10
MA0098.10
MA0100.10.466811
MA0101.10.564269
MA0103.10.28031
MA0105.11.33756
MA0106.10.508314
MA0107.10.185157
MA0108.20.276987
MA0109.10
MA0111.10.513809
MA0113.10.180801
MA0114.10.0677467
MA0115.10.615724
MA0116.11.28009
MA0117.10.437859
MA0119.10.17062
MA0122.11.16324
MA0124.10.578498
MA0125.10.50452
MA0130.10
MA0131.10.217579
MA0132.10
MA0133.10
MA0135.10.431776
MA0136.10.456636
MA0139.10.721254
MA0140.10.121887
MA0141.10.185774
MA0142.10.255934
MA0143.10.180914
MA0144.10.157126
MA0145.10.0995828
MA0146.10.00211819
MA0147.10.380954
MA0148.10.102785
MA0149.10.116654
MA0062.20.00468224
MA0035.20.121502
MA0039.21.67164
MA0138.20.594441
MA0002.20.103088
MA0137.20.0368453
MA0104.20.242912
MA0047.20.162866
MA0112.20.0870721
MA0065.20.105189
MA0150.10.817476
MA0151.10
MA0152.10.395672
MA0153.10.489927
MA0154.10.411721
MA0155.10.138174
MA0156.10.0375332
MA0157.10.236372
MA0158.10
MA0159.10.382591
MA0160.10.110614
MA0161.10
MA0162.10.520472
MA0163.10.107702
MA0164.10.553088
MA0080.20.127678
MA0018.20.983445
MA0099.20.125694
MA0079.20.72007
MA0102.20.895427
MA0258.10.292686
MA0259.10.66181
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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