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MCL coexpression mm9:1604: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005409!6.54e-14!47;UBERON:0009854!1.62e-13!23;UBERON:0009856!1.62e-13!23;UBERON:0002107!3.87e-13!22;UBERON:0007499!3.87e-13!22;UBERON:0006925!3.87e-13!22;UBERON:0009497!3.87e-13!22;UBERON:0000015!3.87e-13!22;UBERON:0002423!3.87e-13!22;UBERON:0006235!3.87e-13!22;UBERON:0008835!3.87e-13!22;UBERON:0003894!3.87e-13!22;UBERON:0004161!3.87e-13!22;UBERON:0008836!3.87e-13!22;UBERON:0002365!1.60e-11!25;UBERON:0002330!1.60e-11!25;UBERON:0005172!6.59e-11!49;UBERON:0005173!6.59e-11!49;UBERON:0002417!6.59e-11!49;UBERON:0000916!6.59e-11!49;UBERON:0000160!4.98e-10!31;UBERON:0004119!5.50e-10!118;UBERON:0000925!5.50e-10!118;UBERON:0006595!5.50e-10!118;UBERON:0001007!8.24e-10!116;UBERON:0001555!8.24e-10!116;UBERON:0007026!8.24e-10!116;UBERON:0004921!2.20e-09!114;UBERON:0004923!2.14e-08!24
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.293744,0.529553,1.46803,0.406364,0.618805,0.715644,0.300268,0.310789,0.370407,0.668936,0.702872,0.300533,0.728641,1.0876,0,0.930881,0.397593,0.283802,0.185796,0.489529,0.145201,0.727684,1.04384,1.32977,0.757752,0.274609,0.641282,0.456327,0.227599,0.626183,1.03545,0.395107,0.253145,1.91085,0.0566307,0.384813,0.699032,0.360612,0.876199,0.401916,1.52768,0.134724,0.426986,0.84962,0.591277,0.847828,1.58288,0.115788,1.16276,0.912738,0.786094,1.17664,1.18062,1.19842,1.74508,0.469329,0.689304,0.26467,1.74061,1.01481,0.796017,0.865544,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.827208,0.152094,1.23259,0.257421,1.96909,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,0.574099,0.618102,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,1.52669,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.0998646,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,3.45739,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,1.39694,1.05179,0.230371,0.133815,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,1.67247,0.745913
}}

Latest revision as of 17:12, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:96805087..96805098,-p3@Pnpo
Mm9::chr11:96805100..96805111,-p4@Pnpo
Mm9::chr11:96805114..96805164,-p2@Pnpo
Mm9::chr11:96805259..96805337,-p1@Pnpo
Mm9::chr12:31596524..31596598,+p1@Sh3yl1


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:0004733pyridoxamine-phosphate oxidase activity0.000832717011300932
GO:0042819vitamin B6 biosynthetic process0.000832717011300932
GO:0008615pyridoxine biosynthetic process0.000832717011300932
GO:0042816vitamin B6 metabolic process0.000832717011300932
GO:0008614pyridoxine metabolic process0.000832717011300932
GO:0010181FMN binding0.00346889380409686
GO:0016641oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor0.00416153195043072
GO:0042364water-soluble vitamin biosynthetic process0.00416153195043072
GO:0009110vitamin biosynthetic process0.00416153195043072
GO:0016638oxidoreductase activity, acting on the CH-NH2 group of donors0.00416153195043072
GO:0006767water-soluble vitamin metabolic process0.00737341938788276
GO:0006766vitamin metabolic process0.0107382485381114
GO:0050662coenzyme binding0.0185179814599571
GO:0048037cofactor binding0.0248679051362699



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
gastrointestinal system6.54e-1447
digestive tract diverticulum1.62e-1323
sac1.62e-1323
liver3.87e-1322
epithelial sac3.87e-1322
digestive gland3.87e-1322
epithelium of foregut-midgut junction3.87e-1322
anatomical boundary3.87e-1322
hepatobiliary system3.87e-1322
foregut-midgut junction3.87e-1322
hepatic diverticulum3.87e-1322
liver primordium3.87e-1322
septum transversum3.87e-1322
liver bud3.87e-1322
exocrine gland1.60e-1125
exocrine system1.60e-1125
abdomen element6.59e-1149
abdominal segment element6.59e-1149
abdominal segment of trunk6.59e-1149
abdomen6.59e-1149
intestine4.98e-1031
endoderm-derived structure5.50e-10118
endoderm5.50e-10118
presumptive endoderm5.50e-10118
digestive system8.24e-10116
digestive tract8.24e-10116
primitive gut8.24e-10116
subdivision of digestive tract2.20e-09114
organ component layer2.14e-0824


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)
MA0003.10.0833043
MA0004.13.6516
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.187732
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.602741
MA0056.10
MA0057.10.192781
MA0058.16.78956
MA0059.15.6131
MA0060.12.4023
MA0061.10.955135
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.000589538
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.148348
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.15.10232
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.11.98468
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.295945
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.157686
MA0146.10.21827
MA0147.12.63204
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.20.285933
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.22.32496
MA0047.20.75686
MA0112.20.47695
MA0065.20.158101
MA0150.13.58052
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.173445
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.0699535
MA0163.10.0644585
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.0167818
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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