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

Latest revision as of 11:04, 17 September 2013


Full id: C245_prostate_penis_salivary_esophagus_kidney_Neutrophils_Pancreatic



Phase1 CAGE Peaks

Hg19::chr11:82843480..82843485,+p@chr11:82843480..82843485
+
Hg19::chr12:102010953..102010982,+p5@MYBPC1
Hg19::chr14:38033393..38033405,+p1@ENST00000554829
Hg19::chr14:74454889..74454892,-p10@ENTPD5
Hg19::chr15:45803320..45803343,+p1@HMGN2P46
Hg19::chr18:56620389..56620397,+p37@ZNF532
Hg19::chr18:56620411..56620421,+p36@ZNF532
Hg19::chr18:56720530..56720541,-p@chr18:56720530..56720541
-
Hg19::chr18:56720695..56720715,-p@chr18:56720695..56720715
-
Hg19::chr19:20432113..20432119,-p@chr19:20432113..20432119
-
Hg19::chr19:36157417..36157420,+p1@UPK1A
Hg19::chr19:51357959..51357992,+p2@KLK3
Hg19::chr19:51358166..51358186,+p1@KLK3
Hg19::chr19:51358195..51358202,+p6@KLK3
Hg19::chr19:51376683..51376701,+p1@KLK2
Hg19::chr19:51379148..51379157,+p9@KLK2
Hg19::chr19:51412603..51412620,-p2@KLK4
Hg19::chr1:58999660..58999680,-p@chr1:58999660..58999680
-
Hg19::chr20:56338330..56338340,-p@chr20:56338330..56338340
-
Hg19::chr20:56338376..56338381,-p@chr20:56338376..56338381
-
Hg19::chr21:42884017..42884035,-p@chr21:42884017..42884035
-
Hg19::chr2:13677795..13677800,+p2@ENST00000434509
Hg19::chr3:107201385..107201388,-p@chr3:107201385..107201388
-
Hg19::chr3:107201513..107201523,-p@chr3:107201513..107201523
-
Hg19::chr3:131978701..131978713,-p@chr3:131978701..131978713
-
Hg19::chr3:131978783..131978794,-p@chr3:131978783..131978794
-
Hg19::chr3:131978834..131978840,-p@chr3:131978834..131978840
-
Hg19::chr3:131978851..131978858,-p@chr3:131978851..131978858
-
Hg19::chr3:131978870..131978881,-p@chr3:131978870..131978881
-
Hg19::chr3:131986361..131986385,-p@chr3:131986361..131986385
-
Hg19::chr3:132036207..132036218,+p3@ACPP
Hg19::chr3:132036243..132036268,+p1@ACPP
Hg19::chr3:44916098..44916104,+p1@TGM4
Hg19::chr4:143522258..143522278,-p@chr4:143522258..143522278
-
Hg19::chr4:80584855..80584865,+p2@ENST00000506460
Hg19::chr4:80584874..80584882,+p3@ENST00000506460
Hg19::chr4:80584903..80584914,+p1@ENST00000506460
Hg19::chr4:95561522..95561531,+p@chr4:95561522..95561531
+
Hg19::chr4:95572086..95572087,+p@chr4:95572086..95572087
+
Hg19::chr5:29485545..29485554,-p@chr5:29485545..29485554
-
Hg19::chr5:59672718..59672753,-p@chr5:59672718..59672753
-
Hg19::chr6:10691162..10691202,+p@chr6:10691162..10691202
+
Hg19::chr6:110964453..110964459,-p16@CDK19
Hg19::chr6:44698851..44698873,+p1@uc003oxm.2
Hg19::chr6:92061457..92061461,-p@chr6:92061457..92061461
-
Hg19::chr7:38313235..38313268,-p1@TRGJP
Hg19::chr7:83218322..83218330,-p@chr7:83218322..83218330
-
Hg19::chr7:89874193..89874199,+p7@C7orf63
Hg19::chr8:1877489..1877493,+p@chr8:1877489..1877493
+
Hg19::chr9:120228535..120228539,-p1@ENST00000436524
Hg19::chr9:5339875..5339881,-p1@RLN1
Hg19::chr9:79379348..79379360,+p1@PCA3
Hg19::chr9:90560553..90560557,+p@chr9:90560553..90560557
+
Hg19::chr9:90562275..90562281,+p@chr9:90562275..90562281
+
Hg19::chrX:24154688..24154714,+p@chrX:24154688..24154714
+


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:0004252serine-type endopeptidase activity0.00752394627533929
GO:0008236serine-type peptidase activity0.00752394627533929
GO:0017171serine hydrolase activity0.00752394627533929
GO:0018184protein amino acid polyamination0.0108177322500883
GO:0004175endopeptidase activity0.0308914333603252
GO:0017110nucleoside-diphosphatase activity0.0308914333603252
GO:0004293tissue kallikrein activity0.0308914333603252



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>uberon_data<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)
MA0003.14.7011e-14
MA0004.10.0230278
MA0006.10.00366578
MA0007.10.419216
MA0009.10.654719
MA0014.13.94999e-08
MA0017.10.214918
MA0019.10.231029
MA0024.10.166016
MA0025.10.326531
MA0027.11.69857
MA0028.10.00464806
MA0029.10.177433
MA0030.11.55952
MA0031.10.418572
MA0038.10.414012
MA0040.13.88396
MA0041.17.27944
MA0042.16.03679
MA0043.10.231848
MA0046.10.224416
MA0048.10.000464638
MA0050.10.227318
MA0051.10.717117
MA0052.10.183297
MA0055.10.00817636
MA0056.10
MA0057.10.0541628
MA0058.10.00874589
MA0059.10.0442201
MA0060.10.0341282
MA0061.10.00145582
MA0063.10
MA0066.10.414788
MA0067.10.473069
MA0068.10.0489211
MA0069.10.221881
MA0070.10.61459
MA0071.10.623423
MA0072.10.211675
MA0073.12.68521e-11
MA0074.10.404998
MA0076.10.0105149
MA0077.10.595956
MA0078.10.286718
MA0081.10.0442917
MA0083.10.236667
MA0084.10.635217
MA0087.10.603971
MA0088.10.0987397
MA0089.10
MA0090.10.816316
MA0091.10.0235515
MA0092.10.632094
MA0093.10.00383862
MA0095.10
MA0098.10
MA0100.10.0538698
MA0101.10.00403286
MA0103.10.0611508
MA0105.10.0190813
MA0106.10.0633877
MA0107.10.00111624
MA0108.20.8218
MA0109.10
MA0111.10.0668683
MA0113.11.34675
MA0114.10.247546
MA0115.10.410377
MA0116.10.00832495
MA0117.10.257218
MA0119.10.228466
MA0122.10.755856
MA0124.10.377376
MA0125.10.841458
MA0130.10
MA0131.10.0923922
MA0132.10
MA0133.10
MA0135.10.70259
MA0136.10.0516336
MA0139.10.00103407
MA0140.10.147406
MA0141.11.70017
MA0142.10.756679
MA0143.11.34746
MA0144.11.21969
MA0145.10.00251586
MA0146.12.83164e-07
MA0147.10.00884099
MA0148.11.20835
MA0149.10.0347551
MA0062.20.000139084
MA0035.20.146798
MA0039.28.68406e-05
MA0138.21.01213
MA0002.20.0276243
MA0137.20.539352
MA0104.20.00280437
MA0047.22.27306
MA0112.20.00490992
MA0065.20.00724468
MA0150.11.11599
MA0151.10
MA0152.10.98886
MA0153.10.300753
MA0154.10.000817593
MA0155.10.00374263
MA0156.10.0292877
MA0157.10.696111
MA0158.10
MA0159.10.280867
MA0160.10.306739
MA0161.10
MA0162.11.39291e-07
MA0163.11.49812e-06
MA0164.10.932619
MA0080.20.0701428
MA0018.20.0638918
MA0099.20.153442
MA0079.21.44649e-16
MA0102.20.668584
MA0258.10.0177501
MA0259.10.0101718
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ESR1#209984.475433206713380.0003859945087645040.00377779781659226
GATA3#262594.456884494815530.0001659500683196420.00204069930357178



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

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