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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.134609515403383,1

Latest revision as of 10:59, 17 September 2013


Full id: C220_Adipocyte_mature_left_breast_skin_liver_adipose



Phase1 CAGE Peaks

Hg19::chr10:102107103..102107119,+p3@SCD
Hg19::chr10:102107865..102107900,-p@chr10:102107865..102107900
-
Hg19::chr10:102107922..102107940,-p@chr10:102107922..102107940
-
Hg19::chr10:102107942..102107961,+p16@SCD
Hg19::chr10:102107962..102107989,-p@chr10:102107962..102107989
-
Hg19::chr10:102120575..102120608,+p@chr10:102120575..102120608
+
Hg19::chr10:102120908..102120961,+p1@ENST00000537595
Hg19::chr10:102121321..102121343,-p1@AF116616
Hg19::chr11:111895937..111895954,+p5@DLAT
Hg19::chr11:111895969..111895977,+p8@DLAT
Hg19::chr11:63273520..63273537,+p2@LGALS12
Hg19::chr11:63273547..63273624,+p1@LGALS12
Hg19::chr11:63273633..63273644,+p3@LGALS12
Hg19::chr11:63273651..63273660,+p7@LGALS12
Hg19::chr11:63273811..63273822,+p6@LGALS12
Hg19::chr11:63273968..63273973,+p12@LGALS12
Hg19::chr11:63381642..63381653,-p11@PLA2G16
Hg19::chr11:77779210..77779221,+p@chr11:77779210..77779221
+
Hg19::chr11:821771..821791,+p6@PNPLA2
Hg19::chr11:821805..821820,+p4@PNPLA2
Hg19::chr11:821969..822000,+p9@PNPLA2
Hg19::chr11:822471..822487,+p8@PNPLA2
Hg19::chr11:823694..823744,+p5@PNPLA2
Hg19::chr11:823806..823819,+p19@PNPLA2
Hg19::chr11:824556..824594,+p@chr11:824556..824594
+
Hg19::chr11:824631..824643,+p@chr11:824631..824643
+
Hg19::chr11:824728..824765,+p@chr11:824728..824765
+
Hg19::chr11:824844..824872,+p@chr11:824844..824872
+
Hg19::chr11:825003..825018,+p@chr11:825003..825018
+
Hg19::chr12:50503990..50504003,+p@chr12:50503990..50504003
+
Hg19::chr12:56102486..56102497,-p@chr12:56102486..56102497
-
Hg19::chr14:74035911..74035922,+p2@ACOT2
Hg19::chr14:74035970..74036005,+p1@ACOT2
Hg19::chr15:90233866..90233883,-p2@PEX11A
Hg19::chr17:17425661..17425669,-p@chr17:17425661..17425669
-
Hg19::chr17:17480330..17480331,-p22@PEMT
Hg19::chr17:17480334..17480356,-p9@PEMT
Hg19::chr17:17480357..17480403,-p4@PEMT
Hg19::chr17:17480405..17480422,-p12@PEMT
Hg19::chr17:17480455..17480488,-p7@PEMT
Hg19::chr17:17480494..17480502,-p15@PEMT
Hg19::chr17:20687991..20688022,-p@chr17:20687991..20688022
-
Hg19::chr17:41003302..41003317,+p3@AOC3
Hg19::chr17:41003393..41003400,+p2@CU690716
Hg19::chr17:41004526..41004533,-p@chr17:41004526..41004533
-
Hg19::chr17:41005283..41005312,+p@chr17:41005283..41005312
+
Hg19::chr17:80049335..80049378,-p@chr17:80049335..80049378
-
Hg19::chr19:4503940..4503950,-p@chr19:4503940..4503950
-
Hg19::chr21:33671160..33671172,+p2@MRAP
Hg19::chr21:33671264..33671281,+p1@MRAP
Hg19::chr2:176046144..176046189,-p2@ATP5G3
Hg19::chr2:176046192..176046216,-p3@ATP5G3
Hg19::chr2:85598470..85598482,+p@chr2:85598470..85598482
+
Hg19::chr3:12200368..12200494,-p1@TIMP4
Hg19::chr3:186572519..186572536,+p@chr3:186572519..186572536
+
Hg19::chr3:9908708..9908727,-p@chr3:9908708..9908727
-
Hg19::chr5:76382989..76383001,-p4@ZBED3
Hg19::chr5:76435018..76435030,+p2@ENST00000511547
p2@ENST00000515356
Hg19::chr6:53187504..53187521,-p@chr6:53187504..53187521
-
Hg19::chr8:19805751..19805767,+p@chr8:19805751..19805767
+
Hg19::chr8:82391739..82391754,-p3@FABP4
Hg19::chr8:82392791..82392838,-p@chr8:82392791..82392838
-
Hg19::chr9:101673536..101673545,+p@chr9:101673536..101673545
+
Hg19::chr9:139580642..139580653,-p@chr9:139580642..139580653
-
Hg19::chrX:2742090..2742104,-p@chrX:2742090..2742104
-
Hg19::chrX:2742111..2742121,-p@chrX:2742111..2742121
-


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
4.66554697163602e-050.029532912330456221Biosynthesis of unsaturated fatty acids (KEGG):01040



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:0044444cytoplasmic part0.0126663134345932
GO:0032787monocarboxylic acid metabolic process0.0126663134345932
GO:0006732coenzyme metabolic process0.0126663134345932
GO:0051186cofactor metabolic process0.0126663134345932
GO:0006629lipid metabolic process0.0126663134345932
GO:0005737cytoplasm0.0126663134345932
GO:0030395lactose binding0.0126663134345932
GO:0004608phosphatidylethanolamine N-methyltransferase activity0.0126663134345932
GO:0005967mitochondrial pyruvate dehydrogenase complex0.0126663134345932
GO:0048030disaccharide binding0.0126663134345932
GO:0005739mitochondrion0.0129812627465017
GO:0045254pyruvate dehydrogenase complex0.0211067938244365
GO:0030523dihydrolipoamide S-acyltransferase activity0.025323679275354
GO:0006085acetyl-CoA biosynthetic process0.025323679275354
GO:0004742dihydrolipoyllysine-residue acetyltransferase activity0.025323679275354
GO:0044429mitochondrial part0.0266517967653305
GO:0001676long-chain fatty acid metabolic process0.0266517967653305
GO:0016418S-acetyltransferase activity0.0266517967653305
GO:0004768stearoyl-CoA 9-desaturase activity0.0266517967653305
GO:0048038quinone binding0.03013658993362
GO:0006656phosphatidylcholine biosynthetic process0.03013658993362
GO:0031090organelle membrane0.0303578874399766
GO:0004091carboxylesterase activity0.0311764867052478
GO:0016559peroxisome fission0.0311764867052478
GO:0006631fatty acid metabolic process0.0311764867052478
GO:0046470phosphatidylcholine metabolic process0.0320330169712323
GO:0008131amine oxidase activity0.0320330169712323
GO:0044255cellular lipid metabolic process0.0320330169712323
GO:0048285organelle fission0.0320330169712323
GO:0016290palmitoyl-CoA hydrolase activity0.0320330169712323
GO:0019752carboxylic acid metabolic process0.0320330169712323
GO:0006082organic acid metabolic process0.0320330169712323
GO:0000038very-long-chain fatty acid metabolic process0.0344957177227504
GO:0016417S-acyltransferase activity0.0361319901495177
GO:0005811lipid particle0.0361319901495177
GO:0031405lipoic acid binding0.0366009477120791
GO:0050729positive regulation of inflammatory response0.0366009477120791
GO:0031349positive regulation of defense response0.0366009477120791
GO:0005783endoplasmic reticulum0.0370001895799611
GO:0005753mitochondrial proton-transporting ATP synthase complex0.0370001895799611
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 water0.0370001895799611
GO:0031406carboxylic acid binding0.0397629278746713
GO:0006954inflammatory response0.0397629278746713
GO:0042632cholesterol homeostasis0.0397629278746713
GO:0055092sterol homeostasis0.0397629278746713
GO:0005779integral to peroxisomal membrane0.0397629278746713
GO:0031231intrinsic to peroxisomal membrane0.0397629278746713
GO:0006637acyl-CoA metabolic process0.0397629278746713
GO:0016021integral to membrane0.0397629278746713
GO:0008191metalloendopeptidase inhibitor activity0.0397629278746713
GO:0004806triacylglycerol lipase activity0.0397629278746713
GO:0045263proton-transporting ATP synthase complex, coupling factor F(o)0.0397629278746713
GO:0033177proton-transporting two-sector ATPase complex, proton-transporting domain0.0397629278746713
GO:0055088lipid homeostasis0.0397629278746713
GO:0031224intrinsic to membrane0.0399045641103036
GO:0008610lipid biosynthetic process0.0407682750111408
GO:0044424intracellular part0.0407682750111408
GO:0043231intracellular membrane-bound organelle0.0407682750111408
GO:0043227membrane-bound organelle0.0407682750111408
GO:0016291acyl-CoA thioesterase activity0.0441758179602411
GO:0045259proton-transporting ATP synthase complex0.0468057706955094
GO:0016641oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor0.0468057706955094
GO:0031347regulation of defense response0.0492685748199168
GO:0050727regulation of inflammatory response0.0492685748199168



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
fat cell5.94e-4915
subcutaneous fat cell6.13e-173
adipocyte of omentum tissue1.21e-163
adipocyte of breast1.31e-112
Uber Anatomy
Ontology termp-valuen
subcutaneous adipose tissue6.13e-173
adult organism2.09e-14114
hypodermis2.38e-105
omentum1.50e-086
peritoneum1.50e-086
abdominal cavity1.50e-086
visceral peritoneum1.50e-086
valve9.55e-083
cardiac mesenchyme9.55e-083
cardial valve9.55e-083
tunica intima9.55e-083
heart layer9.55e-083
endocardium9.55e-083
endocardial cushion9.55e-083
presumptive endocardium9.55e-083


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)
MA0003.10.0287059
MA0004.10.161526
MA0006.10.0843343
MA0007.10.140835
MA0009.10.184704
MA0014.10.0467012
MA0017.10.850488
MA0019.10.164166
MA0024.10.126435
MA0025.10.271833
MA0027.11.62027
MA0028.10.334711
MA0029.10.136417
MA0030.10.130453
MA0031.10.0992614
MA0038.10.551648
MA0040.10.13951
MA0041.10.0151252
MA0042.10.0539025
MA0043.10.184894
MA0046.10.178197
MA0048.10.714709
MA0050.10.147508
MA0051.10.0299809
MA0052.10.141573
MA0055.10.29445
MA0056.10
MA0057.10.397796
MA0058.10.161127
MA0059.10.293755
MA0060.10.000805207
MA0061.10.0411651
MA0063.10
MA0066.11.70709
MA0067.10.410366
MA0068.10.0358039
MA0069.10.521784
MA0070.10.169367
MA0071.10.243203
MA0072.10.965006
MA0073.10.189174
MA0074.10.539436
MA0076.10.778986
MA0077.10.946805
MA0078.10.462602
MA0081.10.977677
MA0083.12.36436
MA0084.10.566927
MA0087.10.49592
MA0088.10.162968
MA0089.10
MA0090.11.89449
MA0091.11.98353
MA0092.11.32573
MA0093.10.0873326
MA0095.10
MA0098.10
MA0100.10.137639
MA0101.10.179817
MA0103.10.843758
MA0105.10.228216
MA0106.10.367333
MA0107.10.0333373
MA0108.20.323094
MA0109.10
MA0111.10.402916
MA0113.10.395506
MA0114.12.45425
MA0115.10.350652
MA0116.10.751874
MA0117.10.207915
MA0119.11.18691
MA0122.10.224541
MA0124.10.319467
MA0125.10.259413
MA0130.10
MA0131.10.0643471
MA0132.10
MA0133.10
MA0135.10.20336
MA0136.10.132172
MA0139.10.273908
MA0140.11.07772
MA0141.10.696667
MA0142.10.289296
MA0143.10.17561
MA0144.10.192028
MA0145.10.157091
MA0146.12.55244
MA0147.10.260575
MA0148.10.191389
MA0149.11.86382
MA0062.20.0368159
MA0035.20.238491
MA0039.20.0691211
MA0138.22.26224
MA0002.20.721787
MA0137.20.209478
MA0104.20.205095
MA0047.20.0381863
MA0112.21.53042
MA0065.21.96718
MA0150.10.817259
MA0151.10
MA0152.10.101154
MA0153.10.247907
MA0154.10.794769
MA0155.10.876902
MA0156.10.21383
MA0157.10.074433
MA0158.10
MA0159.11.57925
MA0160.10.987896
MA0161.10
MA0162.10.00016483
MA0163.10.287639
MA0164.12.10765
MA0080.20.0874187
MA0018.20.161955
MA0099.20.1014
MA0079.20.0679887
MA0102.20.599424
MA0258.11.22275
MA0259.10.284605
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
ESRRA#2101214.66182770109470.008374639402808030.032912096503852
HNF4A#317282.803913983388330.00748083571352610.0308481462899259



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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