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MCL coexpression mm9:1257: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002371!3.79e-10!16;UBERON:0001474!2.26e-09!22;UBERON:0004765!2.26e-09!22;UBERON:0001434!2.26e-09!22;UBERON:0002193!3.28e-09!48;UBERON:0002405!3.28e-09!48;UBERON:0002390!4.53e-09!45;UBERON:0003061!4.53e-09!45;UBERON:0002365!4.49e-08!25;UBERON:0002330!4.49e-08!25;UBERON:0002204!1.83e-07!32;UBERON:0001041!2.32e-07!80;UBERON:0002107!4.57e-07!22;UBERON:0007499!4.57e-07!22;UBERON:0006925!4.57e-07!22;UBERON:0009497!4.57e-07!22;UBERON:0000015!4.57e-07!22;UBERON:0002423!4.57e-07!22;UBERON:0006235!4.57e-07!22;UBERON:0008835!4.57e-07!22;UBERON:0003894!4.57e-07!22;UBERON:0004161!4.57e-07!22;UBERON:0008836!4.57e-07!22
|ontology_enrichment_uberon=UBERON:0002371!3.79e-10!16;UBERON:0001474!2.26e-09!22;UBERON:0004765!2.26e-09!22;UBERON:0001434!2.26e-09!22;UBERON:0002193!3.28e-09!48;UBERON:0002405!3.28e-09!48;UBERON:0002390!4.53e-09!45;UBERON:0003061!4.53e-09!45;UBERON:0002365!4.49e-08!25;UBERON:0002330!4.49e-08!25;UBERON:0002204!1.83e-07!32;UBERON:0001041!2.32e-07!80;UBERON:0002107!4.57e-07!22;UBERON:0007499!4.57e-07!22;UBERON:0006925!4.57e-07!22;UBERON:0009497!4.57e-07!22;UBERON:0000015!4.57e-07!22;UBERON:0002423!4.57e-07!22;UBERON:0006235!4.57e-07!22;UBERON:0008835!4.57e-07!22;UBERON:0003894!4.57e-07!22;UBERON:0004161!4.57e-07!22;UBERON:0008836!4.57e-07!22
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.0600685,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,0.283981,0.599767,0.632897,1.28144,0.6581,0.955327,0,0.856992,0.338549,0.232269,0.143775,0.426133,0.108444,0.657163,0.91309,0.472505,0.686615,0.223823,0.572827,0.394364,0.181062,0.558142,0.960397,0.336199,0.589948,0.364821,0.335531,0.326478,0.629145,0.303703,0.27383,0.342638,0.56353,0.0995018,0.366415,0.659176,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.11437,1.156,0.208101,0.57254,0.204132,0.763395,0.922432,0.430551,1.30789,0.874787,0.722675,0.240896,1.03903,0.0539203,0.827903,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,1.27104,0.976308,0.775372,0.483322,0.326561,0.960112,1.08669,1.95839,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,1.21641,1.0885,1.10269,0.605144,1.33732,0.340765,0.0704207,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,1.25097,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,0.0987301,1.10596,0.287383,0.678689,1.18867,0.71546,0.983048,1.22669,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.86867,1.52669,0.0323861
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.0600685,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,0.283981,0.599767,0.632897,1.28144,0.6581,0.955327,0,0.856992,0.338549,0.232269,0.143775,0.426133,0.108444,0.657163,0.91309,0.472505,0.686615,0.223823,0.572827,0.394364,0.181062,0.558142,0.960397,0.336199,0.589948,0.364821,0.335531,0.326478,0.629145,0.303703,0.27383,0.342638,0.56353,0.0995018,0.366415,0.659176,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.11437,1.156,0.208101,0.57254,0.204132,0.763395,0.922432,0.430551,1.30789,0.874787,0.722675,0.240896,1.03903,0.0539203,0.827903,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,1.27104,0.976308,0.775372,0.483322,0.326561,0.960112,1.08669,1.95839,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,1.21641,1.0885,1.10269,0.605144,1.33732,0.340765,0.0704207,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,1.25097,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,0.0987301,1.10596,0.287383,0.678689,1.18867,0.71546,0.983048,1.22669,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.86867,1.52669,0.0323861
|tfbs_overrepresentation_jaspar=MA0003.1;0.04894,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.0315641,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.370592,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.486223,MA0050.1;0.57678,MA0051.1;1.66123,MA0052.1;1.00829,MA0055.1;0.465302,MA0056.1;0,MA0057.1;0.457693,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;0.275911,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.467569,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.0198269,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;1.19271,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.111145,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;1.25163,MA0093.1;0.379257,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;1.16089,MA0103.1;0.398766,MA0105.1;0.57901,MA0106.1;0.737893,MA0107.1;1.0169,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.359483,MA0117.1;1.05576,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;0.243463,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;0.119202,MA0146.1;0.0392287,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;0.00481054,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;0.261255,MA0047.2;0.685741,MA0112.2;0.119197,MA0065.2;0.119561,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.480757,MA0155.1;0.414701,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.0465447,MA0163.1;0.0423021,MA0164.1;0.658997,MA0080.2;1.01893,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;4.33609e-06,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
}}
}}

Revision as of 13:03, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:87322807..87322831,+p19@Igf1
Mm9::chr15:103163786..103163821,-p@chr15:103163786..103163821
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Mm9::chr2:84371503..84371514,-p3@ENSMUST00000139492
Mm9::chr6:122559982..122559997,-p2@Gdf3
Mm9::chr9:124036273..124036323,+p1@Ccr5
Mm9::chrX:20506928..20506955,-p@chrX:20506928..20506955
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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:0008083growth factor activity0.0163251889016673
GO:0005159insulin-like growth factor receptor binding0.0163251889016673
GO:0018445prothoracicotrophic hormone activity0.0163251889016673
GO:0033143regulation of steroid hormone receptor signaling pathway0.0174836080958784
GO:0050650chondroitin sulfate proteoglycan biosynthetic process0.0174836080958784
GO:0050654chondroitin sulfate proteoglycan metabolic process0.0174836080958784
GO:0030104water homeostasis0.0174836080958784
GO:0018987osmoregulation0.0174836080958784
GO:0021940positive regulation of granule cell precursor proliferation0.0174836080958784
GO:0021936regulation of granule cell precursor proliferation0.0174836080958784
GO:0048009insulin-like growth factor receptor signaling pathway0.0174836080958784
GO:0021534cell proliferation in hindbrain0.0174836080958784
GO:0021924cell proliferation in the external granule layer0.0174836080958784
GO:0021930granule cell precursor proliferation0.0174836080958784
GO:0030518steroid hormone receptor signaling pathway0.021128847713449
GO:0030166proteoglycan biosynthetic process0.021128847713449
GO:0019957C-C chemokine binding0.021128847713449
GO:0016493C-C chemokine receptor activity0.021128847713449
GO:0030522intracellular receptor-mediated signaling pathway0.021128847713449
GO:0005102receptor binding0.021128847713449
GO:0005184neuropeptide hormone activity0.021128847713449
GO:0006029proteoglycan metabolic process0.021128847713449
GO:0030879mammary gland development0.0233974392233283
GO:0004950chemokine receptor activity0.0235162858213455
GO:0019956chemokine binding0.0235162858213455
GO:0001637G-protein chemoattractant receptor activity0.0235162858213455
GO:0044272sulfur compound biosynthetic process0.0262628031664909
GO:0010001glial cell differentiation0.0331679118182337
GO:0042063gliogenesis0.0342078164785799
GO:0030902hindbrain development0.0342078164785799
GO:0048754branching morphogenesis of a tube0.0451191277470559
GO:0006790sulfur metabolic process0.0451191277470559
GO:0035264multicellular organism growth0.0451191277470559
GO:0001763morphogenesis of a branching structure0.0452229396790126
GO:0019955cytokine binding0.0467098664334941
GO:0050878regulation of body fluid levels0.0474379522898477
GO:0048732gland development0.0487826162142913
GO:0006916anti-apoptosis0.049394482355613
GO:0016051carbohydrate biosynthetic process0.049394482355613



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
bone marrow3.79e-1016
bone element2.26e-0922
skeletal element2.26e-0922
skeletal system2.26e-0922
hemolymphoid system3.28e-0948
immune system3.28e-0948
hematopoietic system4.53e-0945
blood island4.53e-0945
exocrine gland4.49e-0825
exocrine system4.49e-0825
musculoskeletal system1.83e-0732
foregut2.32e-0780
liver4.57e-0722
epithelial sac4.57e-0722
digestive gland4.57e-0722
epithelium of foregut-midgut junction4.57e-0722
anatomical boundary4.57e-0722
hepatobiliary system4.57e-0722
foregut-midgut junction4.57e-0722
hepatic diverticulum4.57e-0722
liver primordium4.57e-0722
septum transversum4.57e-0722
liver bud4.57e-0722


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)
MA0003.10.04894
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.10.0315641
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
MA0048.10.486223
MA0050.10.57678
MA0051.11.66123
MA0052.11.00829
MA0055.10.465302
MA0056.10
MA0057.10.457693
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.467569
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.0198269
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.11.19271
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.111145
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.11.25163
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.11.16089
MA0103.10.398766
MA0105.10.57901
MA0106.10.737893
MA0107.11.0169
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.119202
MA0146.10.0392287
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.00481054
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.119197
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.480757
MA0155.10.414701
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.0465447
MA0163.10.0423021
MA0164.10.658997
MA0080.21.01893
MA0018.20.669032
MA0099.20.781628
MA0079.24.33609e-06
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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