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

Latest revision as of 10:57, 17 September 2013


Full id: C211_small_Hepatocyte_liver_colon_temporal_duodenum_kidney



Phase1 CAGE Peaks

Hg19::chr10:135160870..135160906,+p1@PRAP1
Hg19::chr10:135165944..135165963,-p1@CU687189
Hg19::chr10:70066579..70066613,-p4@PBLD
Hg19::chr10:74714533..74714580,-p1@PLA2G12B
Hg19::chr10:96522413..96522424,+p2@CYP2C19
Hg19::chr10:96522430..96522444,+p1@CYP2C19
Hg19::chr11:118900144..118900155,-p6@SLC37A4
Hg19::chr11:118900180..118900195,-p3@SLC37A4
Hg19::chr11:16419067..16419077,-p23@SOX6
Hg19::chr11:17036092..17036106,-p7@PLEKHA7
Hg19::chr11:2924521..2924577,+p2@SLC22A18
Hg19::chr12:56623816..56623825,+p4@SLC39A5
Hg19::chr12:56623827..56623866,+p1@SLC39A5
Hg19::chr14:103561012..103561038,+p2@ENST00000559843
Hg19::chr14:24774871..24774885,-p@chr14:24774871..24774885
-
Hg19::chr14:39703112..39703135,+p1@MIA2
Hg19::chr14:74462922..74462955,-p3@ENTPD5
Hg19::chr15:67356427..67356442,+p@chr15:67356427..67356442
+
Hg19::chr16:27225918..27225945,+p4@JMJD5
Hg19::chr16:583916..583932,+p@chr16:583916..583932
+
Hg19::chr16:66969412..66969439,+p3@CES2
Hg19::chr17:1898875..1898901,+p@chr17:1898875..1898901
+
Hg19::chr19:4164527..4164546,+p@chr19:4164527..4164546
+
Hg19::chr1:100435315..100435325,+p8@SLC35A3
Hg19::chr1:16068987..16069031,+p1@TMEM82
Hg19::chr1:16069036..16069054,+p2@TMEM82
Hg19::chr1:60392452..60392499,-p2@CYP2J2
Hg19::chr1:6511322..6511327,+p21@ESPN
Hg19::chr1:6511328..6511341,+p8@ESPN
Hg19::chr1:6511365..6511371,+p12@ESPN
Hg19::chr20:43024295..43024308,-p1@ENST00000452481
p1@uc002xlx.2
Hg19::chr20:43076886..43076893,+p@chr20:43076886..43076893
+
Hg19::chr21:45287080..45287091,+p9@AGPAT3
Hg19::chr21:45287096..45287111,+p5@AGPAT3
Hg19::chr2:21255446..21255458,-p@chr2:21255446..21255458
-
Hg19::chr2:238499280..238499287,-p7@RAB17
Hg19::chr2:44065897..44065908,-p1@ABCG5
Hg19::chr3:119500874..119500885,+p5@NR1I2
Hg19::chr3:119500891..119500904,+p2@NR1I2
Hg19::chr3:119500908..119500919,+p3@NR1I2
Hg19::chr3:185046677..185046694,+p3@MAP3K13
Hg19::chr3:195943398..195943417,+p1@OSTalpha
Hg19::chr3:58523104..58523127,-p7@ACOX2
Hg19::chr4:22694573..22694609,+p2@GBA3
Hg19::chr4:69817286..69817319,-p2@UGT2A3
Hg19::chr5:149020928..149020943,-p@chr5:149020928..149020943
-
Hg19::chr5:79949935..79949949,-p5@DHFR
Hg19::chr6:133035185..133035201,-p1@VNN1
Hg19::chr6:168227291..168227302,+p19@MLLT4
Hg19::chr6:41006941..41006968,-p1@UNC5CL
Hg19::chr6:43028274..43028300,+p3@KLC4
Hg19::chr6:86099898..86099931,-p1@ENST00000455071
p1@uc003pkm.2
Hg19::chr7:91671935..91671949,+p@chr7:91671935..91671949
+
Hg19::chr7:99277610..99277626,-p1@CYP3A5
Hg19::chr8:110615669..110615692,-p11@SYBU
Hg19::chr8:27348649..27348720,+p1@EPHX2
Hg19::chr8:67624738..67624752,+p10@SGK3
Hg19::chr9:104187248..104187297,-p@chr9:104187248..104187297
-
Hg19::chr9:104187769..104187778,-p3@ALDOB
Hg19::chr9:104187775..104187786,+p@chr9:104187775..104187786
+
Hg19::chr9:104187850..104187863,-p2@ALDOB
Hg19::chr9:104187899..104187908,-p4@ALDOB
Hg19::chr9:104189912..104189930,-p@chr9:104189912..104189930
-
Hg19::chr9:104190749..104190775,+p@chr9:104190749..104190775
+
Hg19::chr9:104192114..104192138,-p@chr9:104192114..104192138
-
Hg19::chr9:104193143..104193169,-p@chr9:104193143..104193169
-
Hg19::chr9:104198042..104198062,-p1@ALDOB
Hg19::chr9:131872789..131872800,-p5@CRAT
Hg19::chr9:32427222..32427240,+p@chr9:32427222..32427240
+
Hg19::chrX:38211890..38211897,+p3@OTC


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
1.15247210510591e-060.000243171614177346459Arachidonic acid metabolism (KEGG):00590
7.13397324646485e-084.51580506501225e-05430Linoleic acid metabolism (KEGG):00591
8.57251743419267e-050.00678300441980495364Retinol metabolism (KEGG):00830
0.0001168451262102020.00767359370758104371Metabolism of xenobiotics by cytochrome P450 (KEGG):00980
0.0001269175009126630.00767359370758104373Drug metabolism - cytochrome P450 (KEGG):00982
4.59754408998177e-050.00485040901493076352Drug metabolism - other enzymes (KEGG):00983
1.72073339083583e-075.44612118199539e-05111138Metabolic pathways (KEGG):01100
0.0001545303115434260.00815147393391574378Peroxisome (KEGG):04146
0.0009985894788454970.0371827729476235Fluoropyrimidine Activity (Wikipathways):WP1601
0.0001333483898631780.00767359370758104213Irinotecan Pathway (Wikipathways):WP229
0.0008876315661719460.0351169238366776233Nuclear receptors in lipid metabolism and toxicity (Wikipathways):WP299
7.42549874428589e-050.00671477243590424361cytochrome P450 (Wikipathways):WP43
3.60830331719628e-050.0045681119995704927Arachidonate Epoxygenase / Epoxide Hydrolase (Wikipathways):WP678
0.000290870553015720.0141631584660731219Tamoxifen metabolism (Wikipathways):WP691
3.48380348952018e-060.0005513119022165685175metapathway biotransformation (Wikipathways):WP702
0.0005791346000023150.02618515727153324289Metabolism of lipids and lipoproteins (Reactome):REACT_22258
0.0006928686483116460.02923905695875153130Biological oxidations (Reactome):REACT_13433



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:0005783endoplasmic reticulum0.000166232769863203
GO:0044255cellular lipid metabolic process0.000292195308455164
GO:0006629lipid metabolic process0.000767639703596833
GO:0044444cytoplasmic part0.000767639703596833
GO:0032787monocarboxylic acid metabolic process0.00101187401991179
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 oxygen0.00101187401991179
GO:0044432endoplasmic reticulum part0.00101187401991179
GO:0019752carboxylic acid metabolic process0.00101187401991179
GO:0006082organic acid metabolic process0.00101187401991179
GO:0006631fatty acid metabolic process0.00254640139128139
GO:0005737cytoplasm0.00548687314804639
GO:0005777peroxisome0.00651008947141174
GO:0042579microbody0.00651008947141174
GO:0050381unspecific monooxygenase activity0.0127585701205273
GO:0042221response to chemical stimulus0.0127585701205273
GO:0006091generation of precursor metabolites and energy0.0134364792462607
GO:0006805xenobiotic metabolic process0.015055976095265
GO:0009410response to xenobiotic stimulus0.0160201134498307
GO:0008374O-acyltransferase activity0.0160201134498307
GO:0005792microsome0.0160201134498307
GO:0042598vesicular fraction0.0160201134498307
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.0160201134498307
GO:0031090organelle membrane0.0160201134498307
GO:0043651linoleic acid metabolic process0.0160201134498307
GO:0008391arachidonic acid monooxygenase activity0.0160201134498307
GO:0009348ornithine carbamoyltransferase complex0.0160201134498307
GO:00337913alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity0.0160201134498307
GO:00038694-nitrophenylphosphatase activity0.0160201134498307
GO:0004092carnitine O-acetyltransferase activity0.0160201134498307
GO:0002532production of molecular mediator of acute inflammatory response0.0160201134498307
GO:0008392arachidonic acid epoxygenase activity0.0160201134498307
GO:0004585ornithine carbamoyltransferase activity0.0160201134498307
GO:0002539prostaglandin production during acute inflammatory response0.0160201134498307
GO:0002538production of arachidonic acid metabolites during acute inflammatory response0.0160201134498307
GO:0005789endoplasmic reticulum membrane0.0200455236898233
GO:0042175nuclear envelope-endoplasmic reticulum network0.020781869242664
GO:0019825oxygen binding0.020781869242664
GO:0008202steroid metabolic process0.020781869242664
GO:0044262cellular carbohydrate metabolic process0.020781869242664
GO:0031667response to nutrient levels0.020781869242664
GO:0004497monooxygenase activity0.020781869242664
GO:0042493response to drug0.020781869242664
GO:0005788endoplasmic reticulum lumen0.020781869242664
GO:0016139glycoside catabolic process0.020781869242664
GO:0018675(S)-limonene 6-monooxygenase activity0.020781869242664
GO:0018676(S)-limonene 7-monooxygenase activity0.020781869242664
GO:0005462UDP-N-acetylglucosamine transmembrane transporter activity0.020781869242664
GO:00337674-hydroxyacetophenone monooxygenase activity0.020781869242664
GO:0015788UDP-N-acetylglucosamine transport0.020781869242664
GO:0019113limonene monooxygenase activity0.020781869242664
GO:0016137glycoside metabolic process0.020781869242664
GO:0017159pantetheinase activity0.020781869242664
GO:0015293symporter activity0.020781869242664
GO:0009991response to extracellular stimulus0.0213609920965642
GO:0000267cell fraction0.0232283299567552
GO:0016020membrane0.0237885008900423
GO:0044446intracellular organelle part0.0245242466769064
GO:0044422organelle part0.0245716351347396
GO:0016413O-acetyltransferase activity0.0267601407488756
GO:0004146dihydrofolate reductase activity0.0267601407488756
GO:0008422beta-glucosidase activity0.0267601407488756
GO:0009056catabolic process0.0284975497610938
GO:0020037heme binding0.0284975497610938
GO:0046906tetrapyrrole binding0.0284975497610938
GO:0008652amino acid biosynthetic process0.0284975497610938
GO:0005351sugar:hydrogen ion symporter activity0.0319907438174286
GO:0045909positive regulation of vasodilation0.0319907438174286
GO:0006545glycine biosynthetic process0.0319907438174286
GO:0012505endomembrane system0.0323882090546499
GO:0051119sugar transmembrane transporter activity0.0336469325662541
GO:0015144carbohydrate transmembrane transporter activity0.0345462005428184
GO:0017110nucleoside-diphosphatase activity0.0357711277698788
GO:0015781pyrimidine nucleotide-sugar transport0.0357711277698788
GO:0010043response to zinc ion0.0357711277698788
GO:0006047UDP-N-acetylglucosamine metabolic process0.0357711277698788
GO:0005543phospholipid binding0.0357711277698788
GO:0006807nitrogen compound metabolic process0.0362188514416722
GO:0005624membrane fraction0.0362188514416722
GO:0008643carbohydrate transport0.0362188514416722
GO:0015165pyrimidine nucleotide sugar transmembrane transporter activity0.0362188514416722
GO:0046688response to copper ion0.0362188514416722
GO:0003997acyl-CoA oxidase activity0.0362188514416722
GO:0004301epoxide hydrolase activity0.0362188514416722
GO:0016406carnitine O-acyltransferase activity0.0362188514416722
GO:0004463leukotriene-A4 hydrolase activity0.0362188514416722
GO:0042301phosphate binding0.0362188514416722
GO:0042312regulation of vasodilation0.0362188514416722
GO:0016743carboxyl- or carbamoyltransferase activity0.0362188514416722
GO:0008385IkappaB kinase complex0.0362188514416722
GO:0017144drug metabolic process0.0362188514416722
GO:0015291secondary active transmembrane transporter activity0.0363783846269499
GO:0043231intracellular membrane-bound organelle0.0363783846269499
GO:0043227membrane-bound organelle0.0363783846269499
GO:0046983protein dimerization activity0.0371343714481092
GO:0015980energy derivation by oxidation of organic compounds0.0371343714481092
GO:0006118electron transport0.0375783309344986
GO:0009309amine biosynthetic process0.0375783309344986
GO:0044424intracellular part0.0401485454015201
GO:0030299cholesterol absorption0.0409602751002365
GO:0019627urea metabolic process0.0409602751002365
GO:0016725oxidoreductase activity, acting on CH or CH2 groups0.0409602751002365
GO:0000050urea cycle0.0409602751002365
GO:0044241lipid digestion0.0409602751002365
GO:0004332fructose-bisphosphate aldolase activity0.0409602751002365
GO:0043603amide metabolic process0.0409602751002365
GO:0016803ether hydrolase activity0.0409602751002365
GO:0015307drug:hydrogen antiporter activity0.0447889839759333
GO:0015904tetracycline transport0.0447889839759333
GO:0015520tetracycline:hydrogen antiporter activity0.0447889839759333
GO:0044464cell part0.0447961671487045
GO:0005975carbohydrate metabolic process0.0455601062325889
GO:0015101organic cation transmembrane transporter activity0.0455601062325889
GO:0050892intestinal absorption0.0455601062325889
GO:00038411-acylglycerol-3-phosphate O-acyltransferase activity0.0455601062325889
GO:0046677response to antibiotic0.0455601062325889
GO:0008493tetracycline transporter activity0.0455601062325889
GO:0045777positive regulation of blood pressure0.0455601062325889
GO:0042895antibiotic transporter activity0.0455601062325889
GO:0031941filamentous actin0.0455601062325889
GO:0044271nitrogen compound biosynthetic process0.0455741786853529
GO:0043229intracellular organelle0.046614361628882
GO:0043226organelle0.046614361628882
GO:0000186activation of MAPKK activity0.0476859990628521
GO:0009070serine family amino acid biosynthetic process0.0476859990628521
GO:0004565beta-galactosidase activity0.0476859990628521
GO:0000287magnesium ion binding0.047781640586173
GO:0042803protein homodimerization activity0.0494110712844477
GO:0008015blood circulation0.0496129124709751
GO:0003013circulatory system process0.0496129124709751
GO:0051384response to glucocorticoid stimulus0.0496129124709751
GO:0015925galactosidase activity0.0496129124709751



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
metabolising cell1.12e-2312
endopolyploid cell1.12e-2312
parenchymal cell1.12e-2312
polyploid cell1.12e-2312
hepatocyte1.12e-2312
endodermal cell9.78e-0858
Uber Anatomy
Ontology termp-valuen
liver3.84e-2619
digestive gland3.84e-2619
liver bud3.84e-2619
epithelium of foregut-midgut junction1.04e-2425
anatomical boundary1.04e-2425
hepatobiliary system1.04e-2425
foregut-midgut junction1.04e-2425
septum transversum1.04e-2425
hepatic diverticulum1.93e-2222
liver primordium1.93e-2222
digestive tract diverticulum2.01e-2123
epithelial sac1.26e-1925
abdomen element3.18e-1954
abdominal segment element3.18e-1954
sac7.82e-1926
abdominal segment of trunk4.26e-1760
abdomen4.26e-1760
gut epithelium4.90e-1654
intestine6.91e-1617
exocrine gland1.25e-1531
exocrine system1.25e-1531
small intestine1.68e-154
endocrine gland1.01e-1335
subdivision of digestive tract1.53e-12118
digestive system3.20e-11145
digestive tract3.20e-11145
primitive gut3.20e-11145
gastrointestinal system7.49e-1125
endocrine system1.95e-1045
endo-epithelium6.15e-1082
endoderm-derived structure6.65e-10160
endoderm6.65e-10160
presumptive endoderm6.65e-10160
gland1.09e-0959
trunk region element2.55e-09101
epididymis4.87e-091
subdivision of trunk3.34e-08112


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)
MA0003.10.00239411
MA0004.10.138771
MA0006.10.026133
MA0007.10.964995
MA0009.10.508818
MA0014.10.000582734
MA0017.112.0045
MA0019.10.337248
MA0024.11.21715
MA0025.10.25504
MA0027.11.59503
MA0028.10.164541
MA0029.11.85768
MA0030.12.44897
MA0031.12.11546
MA0038.10.11044
MA0040.10.400295
MA0041.10.538204
MA0042.10.00871925
MA0043.10.509267
MA0046.11.52294
MA0048.10.0775153
MA0050.11.33854
MA0051.10.489427
MA0052.10.129261
MA0055.10.3399
MA0056.10
MA0057.10.227015
MA0058.10.254524
MA0059.10.0577193
MA0060.10.0973813
MA0061.10.173259
MA0063.10
MA0066.10.268418
MA0067.10.390744
MA0068.10.13906
MA0069.10.162157
MA0070.10.47244
MA0071.10.674702
MA0072.10.909449
MA0073.10.00035895
MA0074.10.106914
MA0076.10.0221401
MA0077.10.149129
MA0078.10.0507386
MA0081.10.252203
MA0083.10.17499
MA0084.10.545308
MA0087.10.46286
MA0088.10.380625
MA0089.10
MA0090.10.176289
MA0091.11.42807
MA0092.11.2077
MA0093.10.0701154
MA0095.10
MA0098.10
MA0100.10.120599
MA0101.10.148906
MA0103.10.985634
MA0105.10.0132555
MA0106.10.330986
MA0107.10.197713
MA0108.20.615972
MA0109.10
MA0111.10.559463
MA0113.11.42405
MA0114.118.6292
MA0115.15.36139
MA0116.10.649993
MA0117.10.193003
MA0119.10.368305
MA0122.10.209091
MA0124.10.301544
MA0125.10.242948
MA0130.10
MA0131.10.206843
MA0132.10
MA0133.10
MA0135.10.188602
MA0136.10.278172
MA0139.10.140928
MA0140.10.083025
MA0141.12.67375
MA0142.10.263523
MA0143.10.155936
MA0144.10.918413
MA0145.11.04581
MA0146.10.208228
MA0147.10.00220865
MA0148.10.330855
MA0149.11.31278
MA0062.20.0261786
MA0035.20.404395
MA0039.20.0749215
MA0138.21.14111
MA0002.20.138005
MA0137.20.468293
MA0104.20.000494081
MA0047.20.311759
MA0112.20.531624
MA0065.23.51526
MA0150.10.16784
MA0151.10
MA0152.10.687022
MA0153.11.89841
MA0154.10.160196
MA0155.10.00865997
MA0156.10.179316
MA0157.10.867142
MA0158.10
MA0159.10.126567
MA0160.10.601688
MA0161.10
MA0162.11.29808e-07
MA0163.10.0312518
MA0164.10.674303
MA0080.20.0273277
MA0018.20.0359876
MA0099.20.21979
MA0079.22.03195e-05
MA0102.20.577493
MA0258.10.845722
MA0259.10.000322258
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#2101213.82400897531790.00937777142594410.0353895237562485
FOXA1#3169172.691201939136470.0001274015715273030.00169477680916317
FOXA2#3170144.926092750533057.37113804995693e-073.27032407306479e-05
HDAC2#3066142.683124047325250.0005809239252178270.00487396479963244
HEY1#23462392.250919009730323.14827382705494e-082.12267637329755e-06
HNF4A#3172268.59199356338285.65805065981129e-181.24666909886082e-15
HNF4G#31742711.09060583162951.6553354100915e-214.47879727706078e-19
RXRA#6256133.728143182981893.77401043834215e-050.0007230854451844



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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