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MCL coexpression mm9:1335: Difference between revisions

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{{MCL_coexpression_mm9
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protein nuclear translocation;0.0429326255162258;20742!GO:0007182;common-partner SMAD protein phosphorylation;0.0429326255162258;20742!GO:0003950;NAD+ ADP-ribosyltransferase activity;0.0429326255162258;52552!GO:0000060;protein import into nucleus, translocation;0.0429326255162258;20742!GO:0051016;barbed-end actin filament capping;0.0429326255162258;20742!GO:0051693;actin filament capping;0.0429326255162258;20742!GO:0030835;negative regulation of actin filament depolymerization;0.0429326255162258;20742!GO:0030834;regulation of actin filament depolymerization;0.0429326255162258;20742!GO:0030042;actin filament depolymerization;0.0429326255162258;20742!GO:0008064;regulation of actin polymerization and/or depolymerization;0.0429326255162258;20742!GO:0051261;protein depolymerization;0.0429326255162258;20742!GO:0032535;regulation of cellular component size;0.0429326255162258;20742!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.0429326255162258;20742!GO:0030832;regulation of actin filament length;0.0429326255162258;20742!GO:0016763;transferase activity, transferring pentosyl groups;0.0429326255162258;52552!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.0429326255162258;20742!GO:0033043;regulation of organelle organization and biogenesis;0.0429326255162258;20742!GO:0051129;negative regulation of cellular component organization and biogenesis;0.0429326255162258;20742!GO:0008154;actin polymerization and/or 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|gostat_on_MCL_coexpression=GO:0007184;SMAD protein nuclear translocation;0.0429326255162258;20742!GO:0007182;common-partner SMAD protein phosphorylation;0.0429326255162258;20742!GO:0003950;NAD+ ADP-ribosyltransferase activity;0.0429326255162258;52552!GO:0000060;protein import into nucleus, translocation;0.0429326255162258;20742!GO:0051016;barbed-end actin filament capping;0.0429326255162258;20742!GO:0051693;actin filament capping;0.0429326255162258;20742!GO:0030835;negative regulation of actin filament depolymerization;0.0429326255162258;20742!GO:0030834;regulation of actin filament depolymerization;0.0429326255162258;20742!GO:0030042;actin filament depolymerization;0.0429326255162258;20742!GO:0008064;regulation of actin polymerization and/or depolymerization;0.0429326255162258;20742!GO:0051261;protein depolymerization;0.0429326255162258;20742!GO:0032535;regulation of cellular component size;0.0429326255162258;20742!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.0429326255162258;20742!GO:0030832;regulation of actin filament length;0.0429326255162258;20742!GO:0016763;transferase activity, transferring pentosyl groups;0.0429326255162258;52552!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.0429326255162258;20742!GO:0033043;regulation of organelle organization and biogenesis;0.0429326255162258;20742!GO:0051129;negative regulation of cellular component organization and biogenesis;0.0429326255162258;20742!GO:0008154;actin polymerization and/or depolymerization;0.0478270065441988;20742!
|ontology_enrichment_celltype=CL:0000988!6.40e-10!32;CL:0002032!6.40e-10!32;CL:0000037!6.40e-10!32;CL:0000566!6.40e-10!32;CL:0000837!6.40e-10!32;CL:0000838!3.79e-08!12;CL:0000084!1.58e-07!11;CL:0000827!1.58e-07!11;CL:0002031!3.09e-07!25;CL:0002320!5.27e-07!46;CL:0000134!5.27e-07!46;CL:0000542!9.26e-07!13;CL:0000051!9.26e-07!13
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!4.88e-15!48;UBERON:0002405!4.88e-15!48;UBERON:0002390!1.60e-13!45;UBERON:0003061!1.60e-13!45;UBERON:0001007!3.56e-12!116;UBERON:0001555!3.56e-12!116;UBERON:0007026!3.56e-12!116;UBERON:0004119!8.98e-12!118;UBERON:0000925!8.98e-12!118;UBERON:0006595!8.98e-12!118;UBERON:0004921!2.06e-11!114;UBERON:0001041!8.58e-10!80;UBERON:0000077!2.90e-09!35;UBERON:0004177!5.68e-09!29;UBERON:0005057!5.68e-09!29;UBERON:0003081!9.51e-08!87;UBERON:0006562!3.33e-07!24;UBERON:0001557!3.33e-07!24;UBERON:0001042!3.33e-07!24;UBERON:0008814!3.33e-07!24;UBERON:0009145!3.33e-07!24;UBERON:0002384!5.27e-07!46;UBERON:0002370!6.70e-07!23;UBERON:0000974!6.70e-07!23;UBERON:0004807!6.70e-07!23;UBERON:0005058!6.70e-07!23;UBERON:0003351!6.70e-07!23;UBERON:0009113!6.70e-07!23;UBERON:0003295!6.70e-07!23;UBERON:0009722!6.70e-07!23;UBERON:0005562!6.70e-07!23;UBERON:0007690!6.70e-07!23
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.473747,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,0.0835344,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.143775,0.426133,0.35122,0.657163,0.91309,0.472505,0.686615,0.223823,0.572827,1.02135,0.181062,0.558142,0.960397,0.336199,0.204204,0.956447,1.36145,0.326478,0.629145,0.303703,2.11759,0.342638,0.56353,0.327433,0.366415,0.368882,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.366795,1.156,0.599223,0.57254,0.589776,0.763395,0.922432,0.430551,0.708505,0.874787,0.722675,0.240896,1.03903,0.0539203,0.0610418,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.244935,0.976308,0.775372,0.160254,0.871473,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.528609,1.33416,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.937314,1.06946,0.52828,1.2285,0.679647,1.35909,0.347287,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,0.183562,0.325363,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,1.25034,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,1.56426,0.63125,0.895201
|tfbs_overrepresentation_jaspar=MA0003.1;0.135108,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.12867,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.969171,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;1.15799,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.486223,MA0050.1;1.41229,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.465302,MA0056.1;0,MA0057.1;0.149949,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;0.911705,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.753052,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.358337,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;0.379257,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;0.398766,MA0105.1;0.199622,MA0106.1;0.737893,MA0107.1;0.392331,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;0.944657,MA0117.1;1.05576,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;2.707,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;0.379391,MA0146.1;0.0392287,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.591842,MA0035.2;0.630778,MA0039.2;0.525037,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;0.132921,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.176524,MA0163.1;1.03138,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.911432,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.833237,MA0442.1;0
}}

Latest revision as of 16:46, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:117814154..117814171,-p7@Parp8
Mm9::chr14:79915502..79915514,+p4@Elf1
Mm9::chr14:79915521..79915539,+p5@Elf1
Mm9::chr17:33102742..33102771,+p1@Zfp472
Mm9::chr1:173612135..173612202,+p1@Cd48
Mm9::chrX:50341332..50341376,+p1@Hprt


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:0007184SMAD protein nuclear translocation0.0429326255162258
GO:0007182common-partner SMAD protein phosphorylation0.0429326255162258
GO:0003950NAD+ ADP-ribosyltransferase activity0.0429326255162258
GO:0000060protein import into nucleus, translocation0.0429326255162258
GO:0051016barbed-end actin filament capping0.0429326255162258
GO:0051693actin filament capping0.0429326255162258
GO:0030835negative regulation of actin filament depolymerization0.0429326255162258
GO:0030834regulation of actin filament depolymerization0.0429326255162258
GO:0030042actin filament depolymerization0.0429326255162258
GO:0008064regulation of actin polymerization and/or depolymerization0.0429326255162258
GO:0051261protein depolymerization0.0429326255162258
GO:0032535regulation of cellular component size0.0429326255162258
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0429326255162258
GO:0030832regulation of actin filament length0.0429326255162258
GO:0016763transferase activity, transferring pentosyl groups0.0429326255162258
GO:0051493regulation of cytoskeleton organization and biogenesis0.0429326255162258
GO:0033043regulation of organelle organization and biogenesis0.0429326255162258
GO:0051129negative regulation of cellular component organization and biogenesis0.0429326255162258
GO:0008154actin polymerization and/or depolymerization0.0478270065441988



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>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
hemolymphoid system4.88e-1548
immune system4.88e-1548
hematopoietic system1.60e-1345
blood island1.60e-1345
digestive system3.56e-12116
digestive tract3.56e-12116
primitive gut3.56e-12116
endoderm-derived structure8.98e-12118
endoderm8.98e-12118
presumptive endoderm8.98e-12118
subdivision of digestive tract2.06e-11114
foregut8.58e-1080
mixed endoderm/mesoderm-derived structure2.90e-0935
hemopoietic organ5.68e-0929
immune organ5.68e-0929
lateral plate mesoderm9.51e-0887
pharynx3.33e-0724
upper respiratory tract3.33e-0724
chordate pharynx3.33e-0724
pharyngeal arch system3.33e-0724
pharyngeal region of foregut3.33e-0724
connective tissue5.27e-0746
thymus6.70e-0723
neck6.70e-0723
respiratory system epithelium6.70e-0723
hemolymphoid system gland6.70e-0723
pharyngeal epithelium6.70e-0723
thymic region6.70e-0723
pharyngeal gland6.70e-0723
entire pharyngeal arch endoderm6.70e-0723
thymus primordium6.70e-0723
early pharyngeal endoderm6.70e-0723


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)
MA0003.10.135108
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.10.12867
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.969171
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.11.15799
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.486223
MA0050.11.41229
MA0051.10.695779
MA0052.11.00829
MA0055.10.465302
MA0056.10
MA0057.10.149949
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.911705
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.753052
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.10.55008
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
MA0114.10.304661
MA0115.11.08851
MA0116.10.944657
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.12.707
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
MA0145.10.379391
MA0146.10.0392287
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.591842
MA0035.20.630778
MA0039.20.525037
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
MA0155.10.132921
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.176524
MA0163.11.03138
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.911432
MA0102.21.7182
MA0258.10.290587
MA0259.10.833237
MA0442.10
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