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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.72572248430102,1

Latest revision as of 11:33, 17 September 2013


Full id: C892_mature_Adipocyte_liver_Hepatocyte_bile_lung_gall



Phase1 CAGE Peaks

Hg19::chr12:16500526..16500542,+p4@MGST1
Hg19::chr12:16500545..16500556,+p3@MGST1
Hg19::chr12:16500571..16500598,+p1@MGST1
Hg19::chr12:16500599..16500618,+p2@MGST1
Hg19::chr12:16507184..16507203,+p7@MGST1
Hg19::chr12:16516767..16516832,+p@chr12:16516767..16516832
+
Hg19::chr12:16516836..16516885,+p@chr12:16516836..16516885
+
Hg19::chr2:85581643..85581663,-p1@RETSAT
Hg19::chr2:85581666..85581696,-p2@RETSAT


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:0031968organelle outer membrane0.000331905677938092
GO:0019867outer membrane0.000331905677938092
GO:0051786all-trans-retinol 13,14-reductase activity0.0016484163428706
GO:0016117carotenoid biosynthetic process0.00269721005288041
GO:0016114terpenoid biosynthetic process0.00269721005288041
GO:0016109tetraterpenoid biosynthetic process0.00269721005288041
GO:0016116carotenoid metabolic process0.00269721005288041
GO:0016108tetraterpenoid metabolic process0.00269721005288041
GO:0031967organelle envelope0.00269721005288041
GO:0031975envelope0.00269721005288041
GO:0042572retinol metabolic process0.00269721005288041
GO:0001523retinoid metabolic process0.0038849809155795
GO:0005640nuclear outer membrane0.0038849809155795
GO:0016101diterpenoid metabolic process0.0038849809155795
GO:0005783endoplasmic reticulum0.00397864652795
GO:0006721terpenoid metabolic process0.0043262649554988
GO:0006776vitamin A metabolic process0.00436255589995717
GO:0006775fat-soluble vitamin metabolic process0.00494393887461995
GO:0006749glutathione metabolic process0.00494393887461995
GO:0031090organelle membrane0.00800270479558612
GO:0008299isoprenoid biosynthetic process0.00800270479558612
GO:0046148pigment biosynthetic process0.00831260284832906
GO:0042440pigment metabolic process0.00889568357393707
GO:0004364glutathione transferase activity0.00889568357393707
GO:0006720isoprenoid metabolic process0.00889568357393707
GO:0019748secondary metabolic process0.0100729845916541
GO:0005741mitochondrial outer membrane0.0135820206985407
GO:0016627oxidoreductase activity, acting on the CH-CH group of donors0.0135820206985407
GO:0016765transferase activity, transferring alkyl or aryl (other than methyl) groups0.0135820206985407
GO:0006766vitamin metabolic process0.0135820206985407
GO:0006790sulfur metabolic process0.0135820206985407
GO:0042445hormone metabolic process0.0135820206985407
GO:0044453nuclear membrane part0.0165535516388697
GO:0050660FAD binding0.0165535516388697
GO:0031965nuclear membrane0.0212881140823036
GO:0005792microsome0.0222008869305807
GO:0042598vesicular fraction0.0225319063857361
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.0229747799532204
GO:0005635nuclear envelope0.0245295652737168
GO:0044446intracellular organelle part0.0302733803357529
GO:0044422organelle part0.0302733803357529
GO:0006732coenzyme metabolic process0.0330957864467546
GO:0050662coenzyme binding0.0330957864467546
GO:0044444cytoplasmic part0.03423899830737
GO:0005743mitochondrial inner membrane0.03423899830737
GO:0019866organelle inner membrane0.0348664034193558
GO:0008610lipid biosynthetic process0.0348664034193558
GO:0051186cofactor metabolic process0.0351600446510186
GO:0031966mitochondrial membrane0.0409301019669531
GO:0048037cofactor binding0.0416234381856567
GO:0005740mitochondrial envelope0.0416234381856567
GO:0005789endoplasmic reticulum membrane0.0432632584406575
GO:0042175nuclear envelope-endoplasmic reticulum network0.043275309226933
GO:0044432endoplasmic reticulum part0.047257146654818



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 cell6.79e-1115
muscle precursor cell7.15e-1058
myoblast7.15e-1058
multi-potent skeletal muscle stem cell7.15e-1058
muscle cell5.28e-0955
fibroblast6.54e-0976
electrically responsive cell3.12e-0861
electrically active cell3.12e-0861
contractile cell5.00e-0859
embryonic cell8.21e-08250
Uber Anatomy
Ontology termp-valuen
trunk8.17e-17199
organism subdivision5.15e-16264
multi-tissue structure8.39e-15342
trunk mesenchyme2.88e-14122
cell layer2.09e-13309
epithelium2.33e-13306
mesenchyme4.93e-13160
entire embryonic mesenchyme4.93e-13160
unilaminar epithelium1.22e-12148
multi-cellular organism1.88e-12656
multilaminar epithelium3.47e-1183
endoderm-derived structure2.29e-10160
endoderm2.29e-10160
presumptive endoderm2.29e-10160
somite4.84e-1071
presomitic mesoderm4.84e-1071
presumptive segmental plate4.84e-1071
dermomyotome4.84e-1071
trunk paraxial mesoderm4.84e-1071
paraxial mesoderm5.07e-1072
presumptive paraxial mesoderm5.07e-1072
dense mesenchyme tissue1.48e-0973
primordium1.61e-09160
anatomical group2.03e-09625
anatomical system2.91e-09624
embryo3.71e-09592
skeletal muscle tissue1.05e-0862
striated muscle tissue1.05e-0862
myotome1.05e-0862
muscle tissue1.46e-0864
musculature1.46e-0864
musculature of body1.46e-0864
immaterial anatomical entity1.59e-08117
anatomical cluster1.71e-08373
epithelial vesicle2.23e-0878
digestive system2.41e-08145
digestive tract2.41e-08145
primitive gut2.41e-08145
embryonic structure3.15e-08564
germ layer4.43e-08560
germ layer / neural crest4.43e-08560
embryonic tissue4.43e-08560
presumptive structure4.43e-08560
germ layer / neural crest derived structure4.43e-08560
epiblast (generic)4.43e-08560
adipose tissue7.91e-0814
developing anatomical structure1.66e-07581
subdivision of digestive tract1.74e-07118
surface structure5.95e-0799
anatomical conduit8.24e-07240


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)
MA0003.10.280999
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.367355
MA0017.10.301634
MA0019.10.558663
MA0024.14.3519
MA0025.11.00397
MA0027.12.48103
MA0028.11.40203
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.42489
MA0056.10
MA0057.10.539841
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.11.20007
MA0072.10.840664
MA0073.10.134844
MA0074.10.509711
MA0076.10.339975
MA0077.11.94461
MA0078.11.47707
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.363555
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.11.31682
MA0105.10.229733
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.11.70852
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.861836
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.046841
MA0146.10.51271
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.833414
MA0035.20.473658
MA0039.20.0189957
MA0138.20.608783
MA0002.20.46405
MA0137.21.42372
MA0104.20.486672
MA0047.20.542971
MA0112.20.0433683
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.0402662
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.502732
MA0163.10.101664
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.48507
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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
HEY1#2346262.693407362070470.009487643473762270.0357434527363198
MYC#460963.48152124773960.002423669811459260.0136558940137566
NANOG#79923412.99767932489450.0001498754873386720.0019312579916303
RDBP#7936234.14186755333890.001478316199753180.00945635239701245
SP1#666763.79892091876060.001506997871138380.0096244940172336
SREBF1#6720631.33723296032557.34199048148931e-095.69257716329816e-07
STAT1#677249.202927776532980.0005628995032252660.00480338763112538
TAF7#687967.622046269949282.97588074999805e-050.000616295874775028
USF1#739164.240999518138640.0008220017441944160.00625995626089548



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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