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

Latest revision as of 11:20, 17 September 2013


Full id: C318_hepatoma_Intestinal_bile_small_colon_Prostate_endometrial



Phase1 CAGE Peaks

Hg19::chr10:5048261..5048285,-p@chr10:5048261..5048285
-
Hg19::chr10:5135981..5136010,+p6@AKR1C3
Hg19::chr11:111154870..111154887,+p2@C11orf53
Hg19::chr11:111154907..111154928,+p1@C11orf53
Hg19::chr11:111154934..111154946,+p3@C11orf53
Hg19::chr11:111154964..111154975,+p4@C11orf53
Hg19::chr11:111175739..111175773,-p6@C11orf92
Hg19::chr11:111175775..111175789,-p7@C11orf92
Hg19::chr11:111176063..111176079,-p8@C11orf92
Hg19::chr11:111176084..111176102,-p9@C11orf92
Hg19::chr11:111176104..111176114,-p11@C11orf92
Hg19::chr11:69715346..69715355,-p@chr11:69715346..69715355
-
Hg19::chr11:69715376..69715382,-p@chr11:69715376..69715382
-
Hg19::chr11:69715408..69715418,-p@chr11:69715408..69715418
-
Hg19::chr14:23445970..23445991,-p6@AJUBA
Hg19::chr14:96734892..96734925,-p1@ENST00000553638
Hg19::chr16:57640858..57640869,-p@chr16:57640858..57640869
-
Hg19::chr19:41509967..41509988,+p3@CYP2B6
Hg19::chr19:41510133..41510160,+p@chr19:41510133..41510160
+
Hg19::chr1:197928283..197928310,+p@chr1:197928283..197928310
+
Hg19::chr3:30226342..30226387,-p@chr3:30226342..30226387
-
Hg19::chr4:72468240..72468271,+p@chr4:72468240..72468271
+
Hg19::chr5:1201465..1201468,+p11@SLC6A19
Hg19::chr5:1201536..1201542,+p4@SLC6A19
Hg19::chr5:1202241..1202252,-p@chr5:1202241..1202252
-
Hg19::chr5:68339691..68339711,-p1@ENST00000479830
Hg19::chr6:132935900..132935911,-p@chr6:132935900..132935911
-
Hg19::chr7:107875370..107875381,-p@chr7:107875370..107875381
-
Hg19::chr8:100519343..100519351,+p@chr8:100519343..100519351
+
Hg19::chr8:100519383..100519390,+p@chr8:100519383..100519390
+
Hg19::chr8:17767866..17767892,-p4@FGL1
Hg19::chr9:22113541..22113546,+p3@CDKN2B-AS
Hg19::chr9:22113608..22113615,+p17@CDKN2B-AS
Hg19::chr9:38437671..38437689,+p@chr9:38437671..38437689
+
Hg19::chr9:38437690..38437712,+p@chr9:38437690..38437712
+
Hg19::chr9:38437716..38437729,+p@chr9:38437716..38437729
+
Hg19::chr9:38437744..38437747,+p@chr9:38437744..38437747
+


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
6.26588234213711e-050.0287703396869713259Arachidonic acid metabolism (KEGG):00590
9.0901547194222e-050.0287703396869713271Metabolism of xenobiotics by cytochrome P450 (KEGG):00980



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:0047017prostaglandin-F synthase activity0.00874172177855952
GO:00470263-alpha-hydroxysteroid dehydrogenase (A-specific) activity0.00874172177855952
GO:0047045testosterone 17-beta-dehydrogenase (NADP+) activity0.00874172177855952
GO:0047115trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity0.00874172177855952
GO:0050327testosterone 17-beta-dehydrogenase activity0.0093240915001036
GO:0005577fibrinogen complex0.0165019362595048
GO:0004033aldo-keto reductase activity0.0165019362595048
GO:0015804neutral amino acid transport0.0165019362595048
GO:0016628oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor0.0165019362595048
GO:0006693prostaglandin metabolic process0.0165019362595048
GO:0006692prostanoid metabolic process0.0165019362595048
GO:0015175neutral amino acid transmembrane transporter activity0.0165019362595048
GO:0006118electron transport0.0201970832734816
GO:0050381unspecific monooxygenase activity0.0216241942435844
GO:0016229steroid dehydrogenase activity0.024833518960349
GO:0006091generation of precursor metabolites and energy0.0272454932255383
GO:0016712oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen0.0306091097628793
GO:0006690icosanoid metabolic process0.0306091097628793
GO:0005328neurotransmitter:sodium symporter activity0.0306091097628793
GO:0005326neurotransmitter transporter activity0.0308192896656132
GO:0015171amino acid transmembrane transporter activity0.034874355006795
GO:0006865amino acid transport0.0369765176591999
GO:0006836neurotransmitter transport0.037764746818911
GO:0016627oxidoreductase activity, acting on the CH-CH group of donors0.037764746818911
GO:0015837amine transport0.037764746818911
GO:0015370solute:sodium symporter activity0.037764746818911
GO:0046943carboxylic acid transmembrane transporter activity0.037764746818911
GO:0046942carboxylic acid transport0.037764746818911
GO:0015849organic acid transport0.037764746818911
GO:0005342organic acid transmembrane transporter activity0.037764746818911
GO:0016491oxidoreductase activity0.037764746818911
GO:0015294solute:cation symporter activity0.0413201004265023



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
epithelial cell of prostate1.12e-173
intestinal epithelial cell1.13e-134
endodermal cell1.42e-0858


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)
MA0003.10.0076786
MA0004.10.227494
MA0006.10.0805392
MA0007.11.20489
MA0009.10.348676
MA0014.11.00699e-05
MA0017.10.266848
MA0019.10.824825
MA0024.10.269509
MA0025.12.01901
MA0027.11.8693
MA0028.10.0920229
MA0029.10.774607
MA0030.11.38351
MA0031.10.649823
MA0038.10.109582
MA0040.10.28793
MA0041.11.36225
MA0042.10.807097
MA0043.10.348924
MA0046.15.43365
MA0048.10.00888689
MA0050.12.26927
MA0051.10.348602
MA0052.10.290795
MA0055.10.0512537
MA0056.10
MA0057.10.0017255
MA0058.10.131305
MA0059.10.562837
MA0060.10.152101
MA0061.10.0463779
MA0063.10
MA0066.10.109799
MA0067.10.617744
MA0068.10.133277
MA0069.10.337164
MA0070.10.328499
MA0071.10.630192
MA0072.10.325036
MA0073.12.51895e-05
MA0074.10.107076
MA0076.10.145686
MA0077.10.854819
MA0078.10.488322
MA0081.10.307799
MA0083.10.354583
MA0084.10.789341
MA0087.10.323157
MA0088.10.0318075
MA0089.10
MA0090.10.159362
MA0091.10.064608
MA0092.10.740914
MA0093.10.0826495
MA0095.10
MA0098.10
MA0100.10.116712
MA0101.10.214833
MA0103.10.620701
MA0105.10.00534552
MA0106.10.131372
MA0107.10.117036
MA0108.20.227449
MA0109.10
MA0111.10.692235
MA0113.10.434
MA0114.10.641939
MA0115.10.549953
MA0116.10.97013
MA0117.10.37852
MA0119.10.279941
MA0122.10.399455
MA0124.10.513817
MA0125.10.442376
MA0130.10
MA0131.10.515467
MA0132.10
MA0133.10
MA0135.10.372723
MA0136.10.734692
MA0139.10.317229
MA0140.12.12043
MA0141.10.128645
MA0142.10.208133
MA0143.10.140623
MA0144.10.206726
MA0145.10.629278
MA0146.10.114703
MA0147.10.125089
MA0148.11.3895
MA0149.10.0851592
MA0062.20.201496
MA0035.22.75067
MA0039.28.38028e-05
MA0138.20.163015
MA0002.20.133452
MA0137.21.07889
MA0104.20.150849
MA0047.21.86128
MA0112.20.0715854
MA0065.20.489181
MA0150.10.99133
MA0151.10
MA0152.10.308851
MA0153.12.86482
MA0154.10.236117
MA0155.10.0307592
MA0156.10.243463
MA0157.10.190314
MA0158.10
MA0159.11.33753
MA0160.10.274469
MA0161.10
MA0162.11.38058e-05
MA0163.10.00194394
MA0164.10.451884
MA0080.20.404801
MA0018.21.3279
MA0099.21.0674
MA0079.21.63601e-11
MA0102.20.824164
MA0258.10.0865304
MA0259.10.277049
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
FOXA2#317063.994129257188960.003515705436370290.0178509776882238
MAFF#2376446.088146647561640.004109374781056080.0195864819623364
MAFK#797553.662261234841880.01113490178151240.040943492136724



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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