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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:20, 17 September 2013


Full id: C330_bronchioalveolar_oral_signet_embryonic_lymphangiectasia_testis_adult



Phase1 CAGE Peaks

Hg19::chr11:106266838..106266843,+p@chr11:106266838..106266843
+
Hg19::chr11:15583363..15583369,+p@chr11:15583363..15583369
+
Hg19::chr11:41809203..41809208,-p@chr11:41809203..41809208
-
Hg19::chr11:69002103..69002105,-p@chr11:69002103..69002105
-
Hg19::chr11:69002371..69002382,-p@chr11:69002371..69002382
-
Hg19::chr11:69002385..69002407,-p@chr11:69002385..69002407
-
Hg19::chr12:47628787..47628808,+p10@FAM113B
Hg19::chr13:111618030..111618074,+p@chr13:111618030..111618074
+
Hg19::chr13:111629545..111629550,+p@chr13:111629545..111629550
+
Hg19::chr13:70823810..70823813,+p@chr13:70823810..70823813
+
Hg19::chr14:36536932..36536937,-p@chr14:36536932..36536937
-
Hg19::chr14:74034310..74034345,+p4@ACOT2
Hg19::chr14:88200641..88200643,-p1@ENST00000556168
Hg19::chr15:40366561..40366568,-p@chr15:40366561..40366568
-
Hg19::chr15:75356166..75356171,+p@chr15:75356166..75356171
+
Hg19::chr17:66077866..66077872,+p@chr17:66077866..66077872
+
Hg19::chr1:166958538..166958552,+p2@MAEL
Hg19::chr1:166964233..166964235,+p@chr1:166964233..166964235
+
Hg19::chr1:87994589..87994604,-p@chr1:87994589..87994604
-
Hg19::chr20:26116667..26116670,+p@chr20:26116667..26116670
+
Hg19::chr3:87647430..87647437,-p@chr3:87647430..87647437
-
Hg19::chr4:169956294..169956301,-p@chr4:169956294..169956301
-
Hg19::chr4:171012844..171012850,-p12@AADAT
Hg19::chr4:42315859..42315864,+p@chr4:42315859..42315864
+
Hg19::chr7:16955191..16955205,+p@chr7:16955191..16955205
+
Hg19::chr7:16955957..16955989,+p@chr7:16955957..16955989
+
Hg19::chr7:4833949..4833955,+p@chr7:4833949..4833955
+
Hg19::chr7:5834097..5834103,+p@chr7:5834097..5834103
+
Hg19::chr8:122157279..122157284,-p@chr8:122157279..122157284
-
Hg19::chr8:144260966..144260967,-p@chr8:144260966..144260967
-
Hg19::chr8:15364131..15364145,-p@chr8:15364131..15364145
-
Hg19::chr9:103785643..103785646,-p@chr9:103785643..103785646
-
Hg19::chr9:79057008..79057019,+p5@GCNT1
Hg19::chr9:87024410..87024417,+p@chr9:87024410..87024417
+
Hg19::chrX:48056224..48056233,-p1@SSX5


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:00475362-aminoadipate transaminase activity0.0128024012211761
GO:0003829beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity0.0128024012211761
GO:0016212kynurenine-oxoglutarate transaminase activity0.0128024012211761
GO:0001676long-chain fatty acid metabolic process0.0128024012211761
GO:0016290palmitoyl-CoA hydrolase activity0.0191979495576364
GO:0000038very-long-chain fatty acid metabolic process0.0191979495576364
GO:0006637acyl-CoA metabolic process0.0292419644481353
GO:0016291acyl-CoA thioesterase activity0.0335726840533861
GO:0016289CoA hydrolase activity0.0369368408147647
GO:0006493protein amino acid O-linked glycosylation0.0383484563431187
GO:0008375acetylglucosaminyltransferase activity0.0489546679572067
GO:0008483transaminase activity0.0489546679572067



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>disease_data<br>

Cell Type
Ontology termp-valuen
pneumocyte1.22e-143
Uber Anatomy
Ontology termp-valuen
bronchoalveolar duct junction3.11e-212
alveolar duct3.11e-212
bronchiole3.11e-212
testis8.12e-218
male reproductive organ1.88e-1511
pulmonary alveolus epithelium1.22e-143
alveolus1.22e-143
pulmonary lobule1.22e-143
lobule1.22e-143
alveolus of lung1.22e-143
alveolar system1.22e-143
pulmonary acinus1.22e-143
alveolar sac1.22e-143
alveolar wall1.22e-143
gonad1.37e-0821
indifferent external genitalia1.37e-0821
indifferent gonad1.37e-0821
gonad primordium1.37e-0821
external genitalia3.04e-0822
male organism3.04e-0822
male reproductive system3.04e-0822
Disease
Ontology termp-valuen
lung adenocarcinoma3.11e-212
non-small cell lung carcinoma2.53e-095
bronchus cancer5.08e-077
bronchogenic carcinoma5.08e-077


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)
MA0003.11.73983e-07
MA0004.10.250106
MA0006.10.0212634
MA0007.10.494381
MA0009.10.366503
MA0014.14.23681e-07
MA0017.10.2976
MA0019.10.145319
MA0024.10.77938
MA0025.10.47683
MA0027.11.89328
MA0028.10.0248137
MA0029.12.25039
MA0030.10.291553
MA0031.11.27023
MA0038.13.93191
MA0040.10.304553
MA0041.10.272403
MA0042.10.234471
MA0043.10.960713
MA0046.10.357837
MA0048.10.00292587
MA0050.10.066352
MA0051.10.118004
MA0052.10.307481
MA0055.10.262593
MA0056.10
MA0057.10.0701724
MA0058.10.148161
MA0059.10.0371511
MA0060.145.6027
MA0061.10.0176627
MA0063.10
MA0066.10.767457
MA0067.10.638784
MA0068.12.15259
MA0069.10.354782
MA0070.10.345954
MA0071.10.329903
MA0072.11.62479
MA0073.10.230656
MA0074.10.117607
MA0076.10.042375
MA0077.10.336397
MA0078.10.175262
MA0081.10.0371987
MA0083.11.72988
MA0084.10.811454
MA0087.10.340509
MA0088.10.143905
MA0089.10
MA0090.10.400602
MA0091.10.0725445
MA0092.10.209949
MA0093.10.236964
MA0095.10
MA0098.10
MA0100.10.127731
MA0101.10.0980277
MA0103.10.217657
MA0105.10.000194889
MA0106.10.14308
MA0107.10.0495017
MA0108.20.680208
MA0109.10
MA0111.10.192269
MA0113.10.152632
MA0114.10.26818
MA0115.10.570409
MA0116.10.0103227
MA0117.10.396851
MA0119.10.311459
MA0122.10.418111
MA0124.11.32163
MA0125.11.16723
MA0130.10
MA0131.10.186723
MA0132.10
MA0133.10
MA0135.10.390959
MA0136.10.124027
MA0139.10.0143415
MA0140.13.60353
MA0141.10.145306
MA0142.10.222682
MA0143.10.464654
MA0144.10.417102
MA0145.10.403141
MA0146.10.00361043
MA0147.10.0107968
MA0148.10.280213
MA0149.10.313847
MA0062.20.0161739
MA0035.22.2286
MA0039.20.152651
MA0138.20.176028
MA0002.20.291191
MA0137.20.50116
MA0104.20.0263481
MA0047.20.836355
MA0112.20.0932543
MA0065.20.42037
MA0150.12.01349
MA0151.10
MA0152.10.684929
MA0153.10.447419
MA0154.10.00704234
MA0155.10.000364621
MA0156.10.507342
MA0157.12.47306
MA0158.10
MA0159.10.0536962
MA0160.11.04124
MA0161.10
MA0162.10.000147124
MA0163.12.95855e-05
MA0164.10.160035
MA0080.20.095553
MA0018.20.143876
MA0099.23.6584
MA0079.26.47482e-06
MA0102.20.846442
MA0258.10.218761
MA0259.10.0581756
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
NFYA#4800147.370232279932211.49137435499956e-091.32446978113775e-07
NFYB#4801125.746214829783934.62112102364577e-072.18778449042856e-05



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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