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MCL coexpression mm9:437: Difference between revisions

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{{MCL_coexpression_mm9
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development;0.00287473216175041;22062,20348!GO:0033326;cerebrospinal fluid secretion;0.0125631121505351;22062!GO:0030215;semaphorin receptor binding;0.0125631121505351;20348!GO:0051864;histone demethylase activity (H3-K36 specific);0.0125631121505351;!GO:0043508;negative regulation of JNK activity;0.0125631121505351;22062!GO:0032452;histone demethylase activity;0.0125631121505351;!GO:0002039;p53 binding;0.018840022401468;22062!GO:0032451;demethylase activity;0.018840022401468;!GO:0045793;positive regulation of cell size;0.018840022401468;22062!GO:0021766;hippocampus development;0.018840022401468;22062!GO:0021761;limbic system development;0.0318673956740005;22062!GO:0001836;release of cytochrome c from mitochondria;0.0318673956740005;22062!GO:0007589;fluid secretion;0.0318673956740005;22062!GO:0048546;digestive tract morphogenesis;0.033219782953293;22062!GO:0021543;pallium development;0.033219782953293;22062!GO:0043506;regulation of JNK activity;0.033219782953293;22062!GO:0001974;blood vessel remodeling;0.033219782953293;20348!GO:0043407;negative regulation of MAP kinase activity;0.033916940711099;22062!GO:0008270;zinc ion binding;0.033916940711099;22062!GO:0008637;apoptotic mitochondrial changes;0.035199655579238;22062!GO:0009887;organ morphogenesis;0.035199655579238;22062,20348!GO:0001755;neural crest cell migration;0.0360566569316459;20348!GO:0043524;negative regulation of neuron apoptosis;0.0360566569316459;22062!GO:0021537;telencephalon development;0.0360566569316459;22062!GO:0016706;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors;0.0376181525092354;!GO:0007399;nervous system development;0.0407061218599463;22062,20348!GO:0014032;neural crest cell development;0.0407061218599463;20348!GO:0014033;neural crest cell differentiation;0.0407061218599463;20348!GO:0046914;transition metal ion 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|gostat_on_MCL_coexpression=GO:0009791;post-embryonic development;0.00287473216175041;22062,20348!GO:0033326;cerebrospinal fluid secretion;0.0125631121505351;22062!GO:0030215;semaphorin receptor binding;0.0125631121505351;20348!GO:0051864;histone demethylase activity (H3-K36 specific);0.0125631121505351;!GO:0043508;negative regulation of JNK activity;0.0125631121505351;22062!GO:0032452;histone demethylase activity;0.0125631121505351;!GO:0002039;p53 binding;0.018840022401468;22062!GO:0032451;demethylase activity;0.018840022401468;!GO:0045793;positive regulation of cell size;0.018840022401468;22062!GO:0021766;hippocampus development;0.018840022401468;22062!GO:0021761;limbic system development;0.0318673956740005;22062!GO:0001836;release of cytochrome c from mitochondria;0.0318673956740005;22062!GO:0007589;fluid secretion;0.0318673956740005;22062!GO:0048546;digestive tract morphogenesis;0.033219782953293;22062!GO:0021543;pallium development;0.033219782953293;22062!GO:0043506;regulation of JNK activity;0.033219782953293;22062!GO:0001974;blood vessel remodeling;0.033219782953293;20348!GO:0043407;negative regulation of MAP kinase activity;0.033916940711099;22062!GO:0008270;zinc ion binding;0.033916940711099;22062!GO:0008637;apoptotic mitochondrial changes;0.035199655579238;22062!GO:0009887;organ morphogenesis;0.035199655579238;22062,20348!GO:0001755;neural crest cell migration;0.0360566569316459;20348!GO:0043524;negative regulation of neuron apoptosis;0.0360566569316459;22062!GO:0021537;telencephalon development;0.0360566569316459;22062!GO:0016706;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors;0.0376181525092354;!GO:0007399;nervous system development;0.0407061218599463;22062,20348!GO:0014032;neural crest cell development;0.0407061218599463;20348!GO:0014033;neural crest cell differentiation;0.0407061218599463;20348!GO:0046914;transition metal ion binding;0.0407061218599463;22062!GO:0043523;regulation of neuron apoptosis;0.0407061218599463;22062!GO:0006469;negative regulation of protein kinase activity;0.0407061218599463;22062!GO:0033673;negative regulation of kinase activity;0.0407061218599463;22062!GO:0051402;neuron apoptosis;0.0407061218599463;22062!GO:0051348;negative regulation of transferase activity;0.0407061218599463;22062!GO:0048762;mesenchymal cell differentiation;0.0407061218599463;20348!GO:0014031;mesenchymal cell development;0.0407061218599463;20348!GO:0007050;cell cycle arrest;0.0456766426830352;22062!GO:0043086;negative regulation of catalytic activity;0.0464436380388674;22062!GO:0008632;apoptotic program;0.0471706680793689;22062!
|ontology_enrichment_celltype=CL:0002609!1.08e-12!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000956!3.28e-10!21;UBERON:0001869!3.28e-10!21;UBERON:0000203!3.28e-10!21;UBERON:0003528!3.01e-09!29;UBERON:0002791!3.01e-09!29;UBERON:0001893!3.01e-09!29;UBERON:0002780!2.34e-08!39;UBERON:0001890!2.34e-08!39;UBERON:0006240!2.34e-08!39;UBERON:0003080!4.08e-08!40;UBERON:0002020!9.93e-08!34;UBERON:0002616!6.97e-07!46
|tfbs_overrepresentation_for_novel_motifs=0.175413,0.00904452,0.476315,0.205657,0.617852,0.618816,0.286882,0.0429524,0.398834,0.260666,0.252112,0.277243,0.376789,0.296787,0.322172,0,0.46143,0.285124,0.147449,0.316699,0.823639,0.208446,0.296055,0.0873986,0.489022,0.319311,0.322606,0.655992,0.114379,0.0210931,0.22152,0.552579,0.0827485,1.19917,0.0978183,0.033615,0.0778621,0.274364,0.237064,0.0536011,1.51347,0.225414,0.182703,0.0986861,0.174452,0.197508,0.391673,0.244272,0.138979,0.37148,0.445973,0.341665,0.217128,0.683824,0.700221,0.302599,0.77262,0.26711,0.302464,0.300938,0.534331,0.349585,0.749563,0.43605,0.311703,1.18928,0.829699,1.16897,0.530087,1.02503,0.144846,0.390307,0.0369163,1.73606,0.0291015,0.263994,0.826666,0.381898,0.518764,0.135947,0.393181,0.476893,0.348372,0.0404688,0.623727,0.000989898,0.00938132,0.715057,0.395899,1.32869,0.896685,0.62835,0.564287,1.56549,0.0649512,0.0567726,0.370414,0.56686,0.391893,0.0158068,0.0779031,0.552324,0.667487,0.446498,0.445567,0.225081,0.498793,0.241171,0.43037,0.134388,0.170493,0.669156,0.424252,0.256145,0.903482,0.60246,0.105429,0.600007,0.462587,0.0759495,0.736964,0.4177,0.320815,1.75967,0.955823,0.522111,0.796971,0.558086,0.828246,0.641535,0.651613,0.200314,0.799981,0.313768,0.92434,0.364618,1.0242,0.226479,0.876916,1.69384,1.29725,0.834212,0.330794,0.562149,0.439856,0.225756,0.394362,1.65442,0.183006,0.299565,0.0950247,0.00478823,1.63944,0.215456,0.313008,0.762455,0.342508,0.104469,0.516355,0.181136,0.886073,0.622933,0.522515,0.168927,0.436947,0.306938,0.266569,0.275979,0.122518
|tfbs_overrepresentation_jaspar=MA0003.1;0.000624928,MA0004.1;0.206012,MA0006.1;0.0950487,MA0007.1;0.195085,MA0009.1;0.576798,MA0014.1;0.00199206,MA0017.1;0.110433,MA0019.1;0.413421,MA0024.1;0.536784,MA0025.1;0.795679,MA0027.1;2.19092,MA0028.1;0.331378,MA0029.1;0.51708,MA0030.1;0.523021,MA0031.1;0.490954,MA0038.1;0.319246,MA0040.1;0.588314,MA0041.1;0.464691,MA0042.1;0.442876,MA0043.1;0.666547,MA0046.1;0.609938,MA0048.1;0.0160841,MA0050.1;0.235075,MA0051.1;0.871644,MA0052.1;0.595747,MA0055.1;0.0306466,MA0056.1;0,MA0057.1;0.0640642,MA0058.1;0.139612,MA0059.1;0.147666,MA0060.1;0.442997,MA0061.1;0.241633,MA0063.1;0,MA0066.1;1.51042,MA0067.1;0.902253,MA0068.1;0.0674589,MA0069.1;0.59606,MA0070.1;0.587119,MA0071.1;0.234437,MA0072.1;0.579318,MA0073.1;4.65699e-06,MA0074.1;0.281183,MA0076.1;0.386726,MA0077.1;2.35617,MA0078.1;0.933078,MA0081.1;0.163204,MA0083.1;0.665805,MA0084.1;1.22195,MA0087.1;0.625609,MA0088.1;0.101322,MA0089.1;0,MA0090.1;0.534933,MA0091.1;0.617309,MA0092.1;0.535473,MA0093.1;0.105788,MA0095.1;0,MA0098.1;0,MA0100.1;0.271974,MA0101.1;0.153616,MA0103.1;0.116929,MA0105.1;0.269753,MA0106.1;0.947606,MA0107.1;0.113208,MA0108.2;0.433384,MA0109.1;0,MA0111.1;0.559312,MA0113.1;0.337108,MA0114.1;0.0673452,MA0115.1;0.669167,MA0116.1;0.0949327,MA0117.1;0.639033,MA0119.1;0.154009,MA0122.1;0.657549,MA0124.1;0.851049,MA0125.1;0.780232,MA0130.1;0,MA0131.1;0.409473,MA0132.1;0,MA0133.1;0,MA0135.1;1.67153,MA0136.1;0.297196,MA0139.1;0.0414323,MA0140.1;0.271883,MA0141.1;0.129134,MA0142.1;0.477975,MA0143.1;0.350815,MA0144.1;0.520464,MA0145.1;0.420675,MA0146.1;0.00335407,MA0147.1;0.0750034,MA0148.1;1.16864,MA0149.1;0.157322,MA0062.2;0.117092,MA0035.2;0.275617,MA0039.2;0.00191438,MA0138.2;0.402586,MA0002.2;0.37393,MA0137.2;0.400341,MA0104.2;0.0483916,MA0047.2;1.54044,MA0112.2;0.420656,MA0065.2;0.241475,MA0150.1;0.195003,MA0151.1;0,MA0152.1;0.318703,MA0153.1;0.716409,MA0154.1;0.366592,MA0155.1;0.138235,MA0156.1;0.121496,MA0157.1;0.4495,MA0158.1;0,MA0159.1;0.0802352,MA0160.1;0.220282,MA0161.1;0,MA0162.1;0.000667848,MA0163.1;0.000516301,MA0164.1;0.297489,MA0080.2;0.365149,MA0018.2;0.305372,MA0099.2;0.397135,MA0079.2;3.62376e-05,MA0102.2;1.27355,MA0258.1;0.219649,MA0259.1;0.0696308,MA0442.1;0
}}

Latest revision as of 15:18, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:69227401..69227417,+p@chr10:69227401..69227417
+
Mm9::chr14:55674497..55674515,+p@chr14:55674497..55674515
+
Mm9::chr14:65036618..65036627,-p@chr14:65036618..65036627
-
Mm9::chr16:42921903..42921908,+p@chr16:42921903..42921908
+
Mm9::chr16:42921959..42921969,+p@chr16:42921959..42921969
+
Mm9::chr16:42921974..42921981,+p@chr16:42921974..42921981
+
Mm9::chr16:77421892..77421903,+p@chr16:77421892..77421903
+
Mm9::chr16:91868147..91868189,+p@chr16:91868147..91868189
+
Mm9::chr18:69679247..69679264,+p@chr18:69679247..69679264
+
Mm9::chr18:69679337..69679354,+p@chr18:69679337..69679354
+
Mm9::chr1:179393159..179393161,-p@chr1:179393159..179393161
-
Mm9::chr2:52182494..52182501,-p@chr2:52182494..52182501
-
Mm9::chr2:77655482..77655519,-p22@Zfp385b
Mm9::chr2:77655548..77655551,-p28@Zfp385b
Mm9::chr4:153471214..153471223,-p3@Trp73
Mm9::chr5:123435005..123435006,-p33@Kdm2b
Mm9::chr5:17080335..17080346,+p12@Sema3c


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:0009791post-embryonic development0.00287473216175041
GO:0033326cerebrospinal fluid secretion0.0125631121505351
GO:0030215semaphorin receptor binding0.0125631121505351
GO:0051864histone demethylase activity (H3-K36 specific)0.0125631121505351
GO:0043508negative regulation of JNK activity0.0125631121505351
GO:0032452histone demethylase activity0.0125631121505351
GO:0002039p53 binding0.018840022401468
GO:0032451demethylase activity0.018840022401468
GO:0045793positive regulation of cell size0.018840022401468
GO:0021766hippocampus development0.018840022401468
GO:0021761limbic system development0.0318673956740005
GO:0001836release of cytochrome c from mitochondria0.0318673956740005
GO:0007589fluid secretion0.0318673956740005
GO:0048546digestive tract morphogenesis0.033219782953293
GO:0021543pallium development0.033219782953293
GO:0043506regulation of JNK activity0.033219782953293
GO:0001974blood vessel remodeling0.033219782953293
GO:0043407negative regulation of MAP kinase activity0.033916940711099
GO:0008270zinc ion binding0.033916940711099
GO:0008637apoptotic mitochondrial changes0.035199655579238
GO:0009887organ morphogenesis0.035199655579238
GO:0001755neural crest cell migration0.0360566569316459
GO:0043524negative regulation of neuron apoptosis0.0360566569316459
GO:0021537telencephalon development0.0360566569316459
GO:0016706oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors0.0376181525092354
GO:0007399nervous system development0.0407061218599463
GO:0014032neural crest cell development0.0407061218599463
GO:0014033neural crest cell differentiation0.0407061218599463
GO:0046914transition metal ion binding0.0407061218599463
GO:0043523regulation of neuron apoptosis0.0407061218599463
GO:0006469negative regulation of protein kinase activity0.0407061218599463
GO:0033673negative regulation of kinase activity0.0407061218599463
GO:0051402neuron apoptosis0.0407061218599463
GO:0051348negative regulation of transferase activity0.0407061218599463
GO:0048762mesenchymal cell differentiation0.0407061218599463
GO:0014031mesenchymal cell development0.0407061218599463
GO:0007050cell cycle arrest0.0456766426830352
GO:0043086negative regulation of catalytic activity0.0464436380388674
GO:0008632apoptotic program0.0471706680793689



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>

Cell Type
Ontology termp-valuen
neuron of cerebral cortex1.08e-126

Uber Anatomy
Ontology termp-valuen
cerebral cortex3.28e-1021
cerebral hemisphere3.28e-1021
pallium3.28e-1021
brain grey matter3.01e-0929
regional part of telencephalon3.01e-0929
telencephalon3.01e-0929
regional part of forebrain2.34e-0839
forebrain2.34e-0839
future forebrain2.34e-0839
anterior neural tube4.08e-0840
gray matter9.93e-0834
regional part of brain6.97e-0746


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)
MA0003.10.000624928
MA0004.10.206012
MA0006.10.0950487
MA0007.10.195085
MA0009.10.576798
MA0014.10.00199206
MA0017.10.110433
MA0019.10.413421
MA0024.10.536784
MA0025.10.795679
MA0027.12.19092
MA0028.10.331378
MA0029.10.51708
MA0030.10.523021
MA0031.10.490954
MA0038.10.319246
MA0040.10.588314
MA0041.10.464691
MA0042.10.442876
MA0043.10.666547
MA0046.10.609938
MA0048.10.0160841
MA0050.10.235075
MA0051.10.871644
MA0052.10.595747
MA0055.10.0306466
MA0056.10
MA0057.10.0640642
MA0058.10.139612
MA0059.10.147666
MA0060.10.442997
MA0061.10.241633
MA0063.10
MA0066.11.51042
MA0067.10.902253
MA0068.10.0674589
MA0069.10.59606
MA0070.10.587119
MA0071.10.234437
MA0072.10.579318
MA0073.14.65699e-06
MA0074.10.281183
MA0076.10.386726
MA0077.12.35617
MA0078.10.933078
MA0081.10.163204
MA0083.10.665805
MA0084.11.22195
MA0087.10.625609
MA0088.10.101322
MA0089.10
MA0090.10.534933
MA0091.10.617309
MA0092.10.535473
MA0093.10.105788
MA0095.10
MA0098.10
MA0100.10.271974
MA0101.10.153616
MA0103.10.116929
MA0105.10.269753
MA0106.10.947606
MA0107.10.113208
MA0108.20.433384
MA0109.10
MA0111.10.559312
MA0113.10.337108
MA0114.10.0673452
MA0115.10.669167
MA0116.10.0949327
MA0117.10.639033
MA0119.10.154009
MA0122.10.657549
MA0124.10.851049
MA0125.10.780232
MA0130.10
MA0131.10.409473
MA0132.10
MA0133.10
MA0135.11.67153
MA0136.10.297196
MA0139.10.0414323
MA0140.10.271883
MA0141.10.129134
MA0142.10.477975
MA0143.10.350815
MA0144.10.520464
MA0145.10.420675
MA0146.10.00335407
MA0147.10.0750034
MA0148.11.16864
MA0149.10.157322
MA0062.20.117092
MA0035.20.275617
MA0039.20.00191438
MA0138.20.402586
MA0002.20.37393
MA0137.20.400341
MA0104.20.0483916
MA0047.21.54044
MA0112.20.420656
MA0065.20.241475
MA0150.10.195003
MA0151.10
MA0152.10.318703
MA0153.10.716409
MA0154.10.366592
MA0155.10.138235
MA0156.10.121496
MA0157.10.4495
MA0158.10
MA0159.10.0802352
MA0160.10.220282
MA0161.10
MA0162.10.000667848
MA0163.10.000516301
MA0164.10.297489
MA0080.20.365149
MA0018.20.305372
MA0099.20.397135
MA0079.23.62376e-05
MA0102.21.27355
MA0258.10.219649
MA0259.10.0696308
MA0442.10
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