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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=-0.

Latest revision as of 14:53, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128397727..128397751,-p@chr10:128397727..128397751
-
Mm9::chr10:61111335..61111384,+p1@Ppa1
Mm9::chr10:80555285..80555291,-p4@Creb3l3
Mm9::chr10:80555299..80555306,-p3@Creb3l3
Mm9::chr11:102006844..102006855,+p2@Nags
Mm9::chr11:120479173..120479195,-p2@Pcyt2
Mm9::chr11:21271267..21271279,-p8@Ugp2
Mm9::chr11:51577156..51577171,+p2@Sar1b
Mm9::chr11:72248736..72248804,+p1@Ggt6
Mm9::chr11:74739427..74739487,-p2@Srr
Mm9::chr12:7984446..7984460,+p1@Apob
Mm9::chr13:40955493..40955508,+p6@Gcnt2
Mm9::chr13:91881112..91881136,+p1@Acot12
Mm9::chr14:66743319..66743342,-p1@Ephx2
Mm9::chr14:70751161..70751242,-p1@Slc39a14
Mm9::chr15:75724662..75724752,-p1@Naprt1
Mm9::chr15:76527155..76527177,+p1@Gpt
Mm9::chr16:20673169..20673190,+p7@Eif4g1
Mm9::chr17:34986829..34986846,+p7@Rdbp
Mm9::chr17:46848408..46848446,+p1@Pex6
Mm9::chr18:12802251..12802331,+p1@Ttc39c
Mm9::chr1:133171854..133171882,-p@chr1:133171854..133171882
-
Mm9::chr1:4797947..4798009,+p1@Lypla1
Mm9::chr2:104582959..104582977,-p1@Depdc7
Mm9::chr2:26459755..26459772,-p1@Agpat2
Mm9::chr2:92215615..92215718,+p1@Pex16
Mm9::chr2:92215861..92215900,+p3@Pex16
Mm9::chr3:94114077..94114093,+p3@Them4
Mm9::chr5:117565891..117565915,-p3@Suds3
Mm9::chr5:30441185..30441192,-p@chr5:30441185..30441192
-
Mm9::chr5:45884688..45884705,+p3@Lap3
Mm9::chr6:124365055..124365096,-p1@Pex5
Mm9::chr6:125181790..125181842,-p3@Tapbpl
Mm9::chr6:149050028..149050111,-p1@Dennd5b
Mm9::chr6:71094357..71094375,-p2@Thnsl2
Mm9::chr6:71149865..71149882,+p1@Fabp1
Mm9::chr7:38968243..38968297,+p2@1600014C10Rik
Mm9::chr7:53128537..53128557,+p3@Kdelr1
Mm9::chr7:88716132..88716204,+p1@Whamm
Mm9::chr9:123217056..123217075,-p1@ENSMUST00000072166
Mm9::chr9:20807189..20807234,+p3@Mrpl4
Mm9::chr9:46036784..46036797,+p1@Apoa1
Mm9::chr9:66823194..66823266,-p1@Lactb
Mm9::chrX:39413565..39413576,+p@chrX:39413565..39413576
+


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

GO IDGO nameFDR corrected p-value
GO:0044444cytoplasmic part0.000282243637853724
GO:0007031peroxisome organization and biogenesis0.00183289316085539
GO:0042579microbody0.00200000199872482
GO:0005777peroxisome0.00200000199872482
GO:0006625protein targeting to peroxisome0.00200000199872482
GO:0043574peroxisomal transport0.00200000199872482
GO:0044255cellular lipid metabolic process0.00200000199872482
GO:0005737cytoplasm0.00318840177491466
GO:0006629lipid metabolic process0.00376957316519926
GO:0005048signal sequence binding0.00496645216233344
GO:0019752carboxylic acid metabolic process0.0054597016437832
GO:0006082organic acid metabolic process0.0054597016437832
GO:0030301cholesterol transport0.00960073583010757
GO:0015918sterol transport0.0102744941563769
GO:0006644phospholipid metabolic process0.0265275240536747
GO:0005783endoplasmic reticulum0.0265275240536747
GO:0003983UTP:glucose-1-phosphate uridylyltransferase activity0.0265275240536747
GO:0017001antibiotic catabolic process0.0265275240536747
GO:0015093ferrous iron transmembrane transporter activity0.0265275240536747
GO:0008800beta-lactamase activity0.0265275240536747
GO:0030655beta-lactam antibiotic catabolic process0.0265275240536747
GO:0051748UDP-sugar pyrophosphorylase activity0.0265275240536747
GO:0016804prolyl aminopeptidase activity0.0265275240536747
GO:0018114threonine racemase activity0.0265275240536747
GO:0004042amino-acid N-acetyltransferase activity0.0265275240536747
GO:0004306ethanolamine-phosphate cytidylyltransferase activity0.0265275240536747
GO:0030653beta-lactam antibiotic metabolic process0.0265275240536747
GO:0030378serine racemase activity0.0265275240536747
GO:0003991acetylglutamate kinase activity0.0265275240536747
GO:0006643membrane lipid metabolic process0.0366001306615916
GO:0009308amine metabolic process0.0366001306615916
GO:0006631fatty acid metabolic process0.0366001306615916
GO:0030170pyridoxal phosphate binding0.0366001306615916
GO:0016740transferase activity0.0366001306615916
GO:0008109N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity0.0366001306615916
GO:0003976UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity0.0366001306615916
GO:0000268peroxisome targeting sequence binding0.0366001306615916
GO:0003986acetyl-CoA hydrolase activity0.0366001306615916
GO:0006642triacylglycerol mobilization0.0366001306615916
GO:0016580Sin3 complex0.0366001306615916
GO:0005046KDEL sequence binding0.0366001306615916
GO:0004795threonine synthase activity0.0366001306615916
GO:0000287magnesium ion binding0.0375876114898993
GO:0006807nitrogen compound metabolic process0.0378655569561019
GO:0008654phospholipid biosynthetic process0.0434664964039327
GO:0008035high-density lipoprotein binding0.0434664964039327
GO:0043534blood vessel endothelial cell migration0.0434664964039327
GO:0004427inorganic diphosphatase activity0.0434664964039327
GO:0016838carbon-oxygen lyase activity, acting on phosphates0.0434664964039327
GO:0016855racemase and epimerase activity, acting on amino acids and derivatives0.0434664964039327
GO:0046923ER retention sequence binding0.0434664964039327
GO:0016558protein import into peroxisome matrix0.0434664964039327
GO:0006621protein retention in ER0.0434664964039327
GO:0032787monocarboxylic acid metabolic process0.0438408156713767
GO:0006520amino acid metabolic process0.0438408156713767
GO:0005779integral to peroxisomal membrane0.0438408156713767
GO:0042826histone deacetylase binding0.0438408156713767
GO:0004178leucyl aminopeptidase activity0.0438408156713767
GO:0007029endoplasmic reticulum organization and biogenesis0.0438408156713767
GO:0002483antigen processing and presentation of endogenous peptide antigen0.0438408156713767
GO:0016999antibiotic metabolic process0.0438408156713767
GO:0033344cholesterol efflux0.0438408156713767
GO:0016812hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides0.0438408156713767
GO:0005381iron ion transmembrane transporter activity0.0438408156713767
GO:0016774phosphotransferase activity, carboxyl group as acceptor0.0438408156713767
GO:0019883antigen processing and presentation of endogenous antigen0.0438408156713767
GO:0030300regulation of cholesterol absorption0.0438408156713767
GO:0006536glutamate metabolic process0.0438408156713767
GO:0021795cerebral cortex cell migration0.0438408156713767
GO:0019885antigen processing and presentation of endogenous peptide antigen via MHC class I0.0438408156713767
GO:0046467membrane lipid biosynthetic process0.0461504408627579
GO:0006869lipid transport0.0479796696453757
GO:0030299cholesterol absorption0.0491359779614124
GO:0051346negative regulation of hydrolase activity0.0491359779614124
GO:0031231intrinsic to peroxisomal membrane0.0491359779614124
GO:0006526arginine biosynthetic process0.0491359779614124
GO:0044241lipid digestion0.0491359779614124
GO:0017144drug metabolic process0.0491359779614124
GO:0008610lipid biosynthetic process0.0496872908318591



Relative expression of the co-expression cluster over median <br>Analyst:




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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
intestine1.17e-1531
digestive tract diverticulum9.58e-1223
sac9.58e-1223
gastrointestinal system2.21e-1147
liver2.67e-1122
epithelial sac2.67e-1122
digestive gland2.67e-1122
epithelium of foregut-midgut junction2.67e-1122
anatomical boundary2.67e-1122
hepatobiliary system2.67e-1122
foregut-midgut junction2.67e-1122
hepatic diverticulum2.67e-1122
liver primordium2.67e-1122
septum transversum2.67e-1122
liver bud2.67e-1122
exocrine gland2.02e-1025
exocrine system2.02e-1025
mucosa4.49e-1015
intestinal mucosa7.02e-0913
anatomical wall7.02e-0913
wall of intestine7.02e-0913
gastrointestinal system mucosa7.02e-0913
endoderm-derived structure1.39e-08118
endoderm1.39e-08118
presumptive endoderm1.39e-08118
digestive system2.89e-08116
digestive tract2.89e-08116
primitive gut2.89e-08116
subdivision of digestive tract1.69e-07114
abdomen element2.49e-0749
abdominal segment element2.49e-0749
abdominal segment of trunk2.49e-0749
abdomen2.49e-0749
trunk mesenchyme2.49e-0745
mesenchyme3.42e-0761
entire embryonic mesenchyme3.42e-0761


TFBS overrepresentation<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)
MA0003.14.52195
MA0004.10.607845
MA0006.10.873758
MA0007.10.896243
MA0009.10.260251
MA0014.15.18355
MA0017.11.75348
MA0019.10.144464
MA0024.10.230104
MA0025.10.439705
MA0027.11.78014
MA0028.12.04036
MA0029.10.215644
MA0030.10.219976
MA0031.10.196896
MA0038.10.619614
MA0040.10.269109
MA0041.10.413962
MA0042.10.383143
MA0043.10.331198
MA0046.10.285948
MA0048.10.610228
MA0050.10.405933
MA0051.11.0663
MA0052.10.754658
MA0055.11.43503
MA0056.10
MA0057.10.699569
MA0058.11.2692
MA0059.11.33889
MA0060.10.495935
MA0061.10.628571
MA0063.10
MA0066.11.00294
MA0067.10.533552
MA0068.11.17122
MA0069.10.27511
MA0070.10.268186
MA0071.10.0477117
MA0072.10.262182
MA0073.14.81869
MA0074.10.521239
MA0076.12.36195
MA0077.10.247052
MA0078.10.350644
MA0081.10.0961027
MA0083.10.330594
MA0084.10.829882
MA0087.10.29831
MA0088.12.68839
MA0089.10
MA0090.10.0277515
MA0091.10.0401384
MA0092.10.0278248
MA0093.10.970722
MA0095.10
MA0098.10
MA0100.10.856308
MA0101.10.417038
MA0103.10.289464
MA0105.10.347738
MA0106.11.75226
MA0107.10.135076
MA0108.20.47642
MA0109.10
MA0111.10.127353
MA0113.10.324571
MA0114.13.13791
MA0115.12.41412
MA0116.10.101542
MA0117.10.832079
MA0119.10.08658
MA0122.10.323899
MA0124.10.488052
MA0125.10.426393
MA0130.10
MA0131.10.861085
MA0132.10
MA0133.10
MA0135.10.359267
MA0136.10.0770147
MA0139.11.94424
MA0140.10.230166
MA0141.10.557067
MA0142.10.187772
MA0143.10.702938
MA0144.10.256406
MA0145.10.59448
MA0146.12.75597
MA0147.11.26867
MA0148.11.44323
MA0149.10.0899707
MA0062.22.52012
MA0035.20.235339
MA0039.25.92286
MA0138.20.137563
MA0002.20.381211
MA0137.20.162668
MA0104.21.44714
MA0047.20.296989
MA0112.21.95262
MA0065.21.1806
MA0150.10.31023
MA0151.10
MA0152.11.03565
MA0153.10.972944
MA0154.10.995578
MA0155.11.93422
MA0156.10.304965
MA0157.10.168226
MA0158.10
MA0159.10.311625
MA0160.11.02652
MA0161.10
MA0162.11.66056
MA0163.12.67736
MA0164.10.26624
MA0080.20.00983331
MA0018.20.0812385
MA0099.20.134134
MA0079.28.15079
MA0102.20.879116
MA0258.12.09708
MA0259.10.639291
MA0442.10
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