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MCL coexpression mm9:207: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!1.17e-15!31;UBERON:0009854!9.58e-12!23;UBERON:0009856!9.58e-12!23;UBERON:0005409!2.21e-11!47;UBERON:0002107!2.67e-11!22;UBERON:0007499!2.67e-11!22;UBERON:0006925!2.67e-11!22;UBERON:0009497!2.67e-11!22;UBERON:0000015!2.67e-11!22;UBERON:0002423!2.67e-11!22;UBERON:0006235!2.67e-11!22;UBERON:0008835!2.67e-11!22;UBERON:0003894!2.67e-11!22;UBERON:0004161!2.67e-11!22;UBERON:0008836!2.67e-11!22;UBERON:0002365!2.02e-10!25;UBERON:0002330!2.02e-10!25;UBERON:0000344!4.49e-10!15;UBERON:0001242!7.02e-09!13;UBERON:0000060!7.02e-09!13;UBERON:0001262!7.02e-09!13;UBERON:0004786!7.02e-09!13;UBERON:0004119!1.39e-08!118;UBERON:0000925!1.39e-08!118;UBERON:0006595!1.39e-08!118;UBERON:0001007!2.89e-08!116;UBERON:0001555!2.89e-08!116;UBERON:0007026!2.89e-08!116;UBERON:0004921!1.69e-07!114;UBERON:0005172!2.49e-07!49;UBERON:0005173!2.49e-07!49;UBERON:0002417!2.49e-07!49;UBERON:0000916!2.49e-07!49;UBERON:0005256!2.49e-07!45;UBERON:0003104!3.42e-07!61;UBERON:0009142!3.42e-07!61
|ontology_enrichment_uberon=UBERON:0000160!1.17e-15!31;UBERON:0009854!9.58e-12!23;UBERON:0009856!9.58e-12!23;UBERON:0005409!2.21e-11!47;UBERON:0002107!2.67e-11!22;UBERON:0007499!2.67e-11!22;UBERON:0006925!2.67e-11!22;UBERON:0009497!2.67e-11!22;UBERON:0000015!2.67e-11!22;UBERON:0002423!2.67e-11!22;UBERON:0006235!2.67e-11!22;UBERON:0008835!2.67e-11!22;UBERON:0003894!2.67e-11!22;UBERON:0004161!2.67e-11!22;UBERON:0008836!2.67e-11!22;UBERON:0002365!2.02e-10!25;UBERON:0002330!2.02e-10!25;UBERON:0000344!4.49e-10!15;UBERON:0001242!7.02e-09!13;UBERON:0000060!7.02e-09!13;UBERON:0001262!7.02e-09!13;UBERON:0004786!7.02e-09!13;UBERON:0004119!1.39e-08!118;UBERON:0000925!1.39e-08!118;UBERON:0006595!1.39e-08!118;UBERON:0001007!2.89e-08!116;UBERON:0001555!2.89e-08!116;UBERON:0007026!2.89e-08!116;UBERON:0004921!1.69e-07!114;UBERON:0005172!2.49e-07!49;UBERON:0005173!2.49e-07!49;UBERON:0002417!2.49e-07!49;UBERON:0000916!2.49e-07!49;UBERON:0005256!2.49e-07!45;UBERON:0003104!3.42e-07!61;UBERON:0009142!3.42e-07!61
|tfbs_overrepresentation_for_novel_motifs=0.794677,0.363745,0.430626,0.144193,0.0899833,0.157279,0.535804,0.384906,0.153535,1.6697,0.20331,0.0670848,0.385817,0.561263,0.10616,0,0.522802,0.329859,0.492321,1.0494,0.174661,0.49601,2.55872,0.0885618,0.728448,0.298017,0.301016,0.177214,1.04749,1.50761,0.163695,0.678623,0.76121,0.722799,1.22056,0.0848419,0.716031,0.865427,0.130593,0.184586,0.0862982,0.168596,0.212659,0.228917,1.67233,0.908763,0.409098,0.428539,0.0507254,0.751163,0.497135,0.678642,1.7141,0.345318,0.358841,0.2736,0.151391,0.485548,0.412337,0.967226,0.22829,0.343503,0.67656,0.480792,1.00866,0.183542,0.469298,0.779659,0.22516,0.645209,0.948635,0.25832,0.294637,0.385253,1.24303,0.488992,0.237661,0.124708,0.21687,0.180201,0.0731719,1.04698,0.104831,0.360806,0.296819,1.29381,0.0330183,1.23281,0.13336,0.932016,0.528571,1.47542,0.250717,0.0955531,0.124972,0.517765,0.0637794,0.703636,0.409447,0.306558,0.716411,0.678177,0.331962,0.166205,0.16558,1.05134,0.585809,0.188857,0.365753,0.876873,0.0242896,0.333321,0.181699,0.796092,0.534653,0.185522,2.32644,1.37905,0.177127,0.471305,0.389556,0.14722,0.0894506,0.124234,0.581865,0.219311,0.55269,0.246028,0.468027,0.591365,0.319105,0.137799,0.443426,0.289861,0.553389,0.0325673,0.517011,0.169944,1.2728,1.28785,0.901817,1.1922,0.315088,0.249098,0.161761,0.0441266,0.413373,1.24909,0.523117,0.820479,2.17671,1.07117,0.915958,0.543487,0.288747,0.411175,0.332734,0.247849,0.107377,0.516289,0.519098,0.29619,0.626457,0.102202,0.159827,0.082057,1.30121,0.235842,3.36017
}}
}}

Revision as of 17:59, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128397727..128397751,-p@chr10:128397727..128397751
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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
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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
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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)

{{{tfbs_overrepresentation_jaspar}}}

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