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MCL coexpression mm9:1228: Difference between revisions

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{{MCL_coexpression_mm9
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transaminase activity;0.0041634709950561;268860!GO:0004155;6,7-dihydropteridine reductase activity;0.0041634709950561;110391!GO:0003867;4-aminobutyrate transaminase activity;0.0041634709950561;268860!GO:0004359;glutaminase activity;0.0041634709950561;216456!GO:0009448;gamma-aminobutyric acid metabolic process;0.0041634709950561;268860!GO:0019605;butyrate metabolic process;0.0041634709950561;268860!GO:0046459;short-chain fatty acid metabolic process;0.00535274084634663;268860!GO:0006519;amino acid and derivative metabolic process;0.00624383788019355;268860,216456!GO:0009308;amine metabolic process;0.00624383788019355;268860,216456!GO:0046146;tetrahydrobiopterin metabolic process;0.00624383788019355;110391!GO:0006729;tetrahydrobiopterin biosynthetic process;0.00624383788019355;110391!GO:0048148;behavioral response to cocaine;0.00624383788019355;268860!GO:0006807;nitrogen compound metabolic process;0.00645743380769793;268860,216456!GO:0042220;response to cocaine;0.00713346895609554;268860!GO:0014073;response to tropane;0.00713346895609554;268860!GO:0042135;neurotransmitter catabolic process;0.00713346895609554;268860!GO:0019752;carboxylic acid metabolic process;0.00713346895609554;268860,216456!GO:0006082;organic acid metabolic process;0.00713346895609554;268860,216456!GO:0016646;oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor;0.00713346895609554;110391!GO:0042559;pteridine and derivative biosynthetic process;0.00713346895609554;110391!GO:0019438;aromatic compound biosynthetic process;0.00713346895609554;110391!GO:0042558;pteridine and derivative metabolic process;0.00737625116058902;110391!GO:0006541;glutamine metabolic process;0.00814012073937108;216456!GO:0014070;response to organic cyclic substance;0.00832055629888129;268860!GO:0043279;response to alkaloid;0.00848650230913251;268860!GO:0016645;oxidoreductase activity, acting on the CH-NH group of donors;0.0095985374026547;110391!GO:0008483;transaminase activity;0.0124733118923655;268860!GO:0010033;response to organic substance;0.0129013042874089;268860!GO:0009064;glutamine family amino acid metabolic process;0.0129013042874089;216456!GO:0016769;transferase activity, transferring nitrogenous groups;0.0145458166495335;268860!GO:0042133;neurotransmitter metabolic process;0.0148793421196347;268860!GO:0005739;mitochondrion;0.0173689385913227;268860,216456!GO:0030170;pyridoxal phosphate binding;0.0173689385913227;268860!GO:0016811;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides;0.0175891186569008;216456!GO:0030534;adult behavior;0.0216987099500702;268860!GO:0006575;amino acid derivative metabolic process;0.0294401520806833;268860!GO:0001505;regulation of neurotransmitter levels;0.0294401520806833;268860!GO:0016810;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds;0.0294401520806833;216456!GO:0019842;vitamin 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|gostat_on_MCL_coexpression=GO:0047298;(S)-3-amino-2-methylpropionate transaminase activity;0.0041634709950561;268860!GO:0004155;6,7-dihydropteridine reductase activity;0.0041634709950561;110391!GO:0003867;4-aminobutyrate transaminase activity;0.0041634709950561;268860!GO:0004359;glutaminase activity;0.0041634709950561;216456!GO:0009448;gamma-aminobutyric acid metabolic process;0.0041634709950561;268860!GO:0019605;butyrate metabolic process;0.0041634709950561;268860!GO:0046459;short-chain fatty acid metabolic process;0.00535274084634663;268860!GO:0006519;amino acid and derivative metabolic process;0.00624383788019355;268860,216456!GO:0009308;amine metabolic process;0.00624383788019355;268860,216456!GO:0046146;tetrahydrobiopterin metabolic process;0.00624383788019355;110391!GO:0006729;tetrahydrobiopterin biosynthetic process;0.00624383788019355;110391!GO:0048148;behavioral response to cocaine;0.00624383788019355;268860!GO:0006807;nitrogen compound metabolic process;0.00645743380769793;268860,216456!GO:0042220;response to cocaine;0.00713346895609554;268860!GO:0014073;response to tropane;0.00713346895609554;268860!GO:0042135;neurotransmitter catabolic process;0.00713346895609554;268860!GO:0019752;carboxylic acid metabolic process;0.00713346895609554;268860,216456!GO:0006082;organic acid metabolic process;0.00713346895609554;268860,216456!GO:0016646;oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor;0.00713346895609554;110391!GO:0042559;pteridine and derivative biosynthetic process;0.00713346895609554;110391!GO:0019438;aromatic compound biosynthetic process;0.00713346895609554;110391!GO:0042558;pteridine and derivative metabolic process;0.00737625116058902;110391!GO:0006541;glutamine metabolic process;0.00814012073937108;216456!GO:0014070;response to organic cyclic substance;0.00832055629888129;268860!GO:0043279;response to alkaloid;0.00848650230913251;268860!GO:0016645;oxidoreductase activity, acting on the CH-NH group of donors;0.0095985374026547;110391!GO:0008483;transaminase activity;0.0124733118923655;268860!GO:0010033;response to organic substance;0.0129013042874089;268860!GO:0009064;glutamine family amino acid metabolic process;0.0129013042874089;216456!GO:0016769;transferase activity, transferring nitrogenous groups;0.0145458166495335;268860!GO:0042133;neurotransmitter metabolic process;0.0148793421196347;268860!GO:0005739;mitochondrion;0.0173689385913227;268860,216456!GO:0030170;pyridoxal phosphate binding;0.0173689385913227;268860!GO:0016811;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides;0.0175891186569008;216456!GO:0030534;adult behavior;0.0216987099500702;268860!GO:0006575;amino acid derivative metabolic process;0.0294401520806833;268860!GO:0001505;regulation of neurotransmitter levels;0.0294401520806833;268860!GO:0016810;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds;0.0294401520806833;216456!GO:0019842;vitamin binding;0.0334386147345175;268860!GO:0006725;aromatic compound metabolic process;0.0350712547476216;110391!GO:0006631;fatty acid metabolic process;0.0483223287291328;268860!GO:0048037;cofactor binding;0.049508617140918;268860!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0009854!2.78e-08!23;UBERON:0009856!2.78e-08!23;UBERON:0002107!4.54e-08!22;UBERON:0007499!4.54e-08!22;UBERON:0006925!4.54e-08!22;UBERON:0009497!4.54e-08!22;UBERON:0000015!4.54e-08!22;UBERON:0002423!4.54e-08!22;UBERON:0006235!4.54e-08!22;UBERON:0008835!4.54e-08!22;UBERON:0003894!4.54e-08!22;UBERON:0004161!4.54e-08!22;UBERON:0008836!4.54e-08!22;UBERON:0005172!2.28e-07!49;UBERON:0005173!2.28e-07!49;UBERON:0002417!2.28e-07!49;UBERON:0000916!2.28e-07!49
}}

Latest revision as of 16:35, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:127631777..127631811,+p2@Gls2
Mm9::chr16:8513565..8513590,+p1@Abat
Mm9::chr5:45841360..45841378,-p2@Qdpr
Mm9::chr5:45841382..45841440,-p1@Qdpr
Mm9::chr7:114711161..114711222,+p2@Olfml1
Mm9::chr7:114711232..114711260,+p4@Olfml1


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:0047298(S)-3-amino-2-methylpropionate transaminase activity0.0041634709950561
GO:00041556,7-dihydropteridine reductase activity0.0041634709950561
GO:00038674-aminobutyrate transaminase activity0.0041634709950561
GO:0004359glutaminase activity0.0041634709950561
GO:0009448gamma-aminobutyric acid metabolic process0.0041634709950561
GO:0019605butyrate metabolic process0.0041634709950561
GO:0046459short-chain fatty acid metabolic process0.00535274084634663
GO:0006519amino acid and derivative metabolic process0.00624383788019355
GO:0009308amine metabolic process0.00624383788019355
GO:0046146tetrahydrobiopterin metabolic process0.00624383788019355
GO:0006729tetrahydrobiopterin biosynthetic process0.00624383788019355
GO:0048148behavioral response to cocaine0.00624383788019355
GO:0006807nitrogen compound metabolic process0.00645743380769793
GO:0042220response to cocaine0.00713346895609554
GO:0014073response to tropane0.00713346895609554
GO:0042135neurotransmitter catabolic process0.00713346895609554
GO:0019752carboxylic acid metabolic process0.00713346895609554
GO:0006082organic acid metabolic process0.00713346895609554
GO:0016646oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor0.00713346895609554
GO:0042559pteridine and derivative biosynthetic process0.00713346895609554
GO:0019438aromatic compound biosynthetic process0.00713346895609554
GO:0042558pteridine and derivative metabolic process0.00737625116058902
GO:0006541glutamine metabolic process0.00814012073937108
GO:0014070response to organic cyclic substance0.00832055629888129
GO:0043279response to alkaloid0.00848650230913251
GO:0016645oxidoreductase activity, acting on the CH-NH group of donors0.0095985374026547
GO:0008483transaminase activity0.0124733118923655
GO:0010033response to organic substance0.0129013042874089
GO:0009064glutamine family amino acid metabolic process0.0129013042874089
GO:0016769transferase activity, transferring nitrogenous groups0.0145458166495335
GO:0042133neurotransmitter metabolic process0.0148793421196347
GO:0005739mitochondrion0.0173689385913227
GO:0030170pyridoxal phosphate binding0.0173689385913227
GO:0016811hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides0.0175891186569008
GO:0030534adult behavior0.0216987099500702
GO:0006575amino acid derivative metabolic process0.0294401520806833
GO:0001505regulation of neurotransmitter levels0.0294401520806833
GO:0016810hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.0294401520806833
GO:0019842vitamin binding0.0334386147345175
GO:0006725aromatic compound metabolic process0.0350712547476216
GO:0006631fatty acid metabolic process0.0483223287291328
GO:0048037cofactor binding0.049508617140918



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
digestive tract diverticulum2.78e-0823
sac2.78e-0823
liver4.54e-0822
epithelial sac4.54e-0822
digestive gland4.54e-0822
epithelium of foregut-midgut junction4.54e-0822
anatomical boundary4.54e-0822
hepatobiliary system4.54e-0822
foregut-midgut junction4.54e-0822
hepatic diverticulum4.54e-0822
liver primordium4.54e-0822
septum transversum4.54e-0822
liver bud4.54e-0822
abdomen element2.28e-0749
abdominal segment element2.28e-0749
abdominal segment of trunk2.28e-0749
abdomen2.28e-0749


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)
MA0003.11.03722
MA0004.10.536396
MA0006.10.945134
MA0007.10.52077
MA0009.10.987341
MA0014.10.558098
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.895081
MA0058.10.436487
MA0059.10.449345
MA0060.12.1282
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.14.40866
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.12.12135
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.725434
MA0089.10
MA0090.10.500693
MA0091.12.32562
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.822296
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.11.8691
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.11.2655
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.761789
MA0146.10.353523
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.22.61252
MA0138.20.788113
MA0002.20.246463
MA0137.21.06926
MA0104.20.261255
MA0047.20.685741
MA0112.20.37938
MA0065.20.763394
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.11.49271
MA0155.10.132921
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.397553
MA0163.11.4645
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.25.82723
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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