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MCL coexpression mm9:822: Difference between revisions

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{{MCL_coexpression_mm9
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domain binding;0.031311569005268;16825!GO:0045647;negative regulation of erythrocyte differentiation;0.031311569005268;16825!GO:0003828;alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity;0.031311569005268;20449!GO:0021692;cerebellar Purkinje cell layer morphogenesis;0.031311569005268;16825!GO:0045646;regulation of erythrocyte differentiation;0.031311569005268;16825!GO:0021694;cerebellar Purkinje cell layer formation;0.031311569005268;16825!GO:0021702;cerebellar Purkinje cell differentiation;0.031311569005268;16825!GO:0007264;small GTPase mediated signal transduction;0.031311569005268;16801,246710!GO:0009948;anterior/posterior axis specification;0.031311569005268;16825!GO:0021697;cerebellar cortex formation;0.031311569005268;16825!GO:0021533;cell differentiation in hindbrain;0.031311569005268;16825!GO:0021680;cerebellar Purkinje cell layer development;0.0329351728611453;16825!GO:0021696;cerebellar cortex morphogenesis;0.0329351728611453;16825!GO:0021587;cerebellum morphogenesis;0.0329351728611453;16825!GO:0021575;hindbrain morphogenesis;0.0329351728611453;16825!GO:0009798;axis specification;0.0329351728611453;16825!GO:0021695;cerebellar cortex development;0.0329351728611453;16825!GO:0045638;negative regulation of myeloid cell differentiation;0.0329351728611453;16825!GO:0008373;sialyltransferase activity;0.0329351728611453;20449!GO:0022037;metencephalon development;0.0339951706826381;16825!GO:0021549;cerebellum development;0.0339951706826381;16825!GO:0030173;integral to Golgi membrane;0.0339951706826381;20449!GO:0031228;intrinsic to Golgi membrane;0.0339951706826381;20449!GO:0001702;gastrulation with mouth forming second;0.040377673861967;16825!GO:0045637;regulation of myeloid cell differentiation;0.0437497994423553;16825!GO:0030218;erythrocyte differentiation;0.0444636384954912;16825!GO:0030902;hindbrain 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|gostat_on_MCL_coexpression=GO:0030274;LIM domain binding;0.031311569005268;16825!GO:0045647;negative regulation of erythrocyte differentiation;0.031311569005268;16825!GO:0003828;alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity;0.031311569005268;20449!GO:0021692;cerebellar Purkinje cell layer morphogenesis;0.031311569005268;16825!GO:0045646;regulation of erythrocyte differentiation;0.031311569005268;16825!GO:0021694;cerebellar Purkinje cell layer formation;0.031311569005268;16825!GO:0021702;cerebellar Purkinje cell differentiation;0.031311569005268;16825!GO:0007264;small GTPase mediated signal transduction;0.031311569005268;16801,246710!GO:0009948;anterior/posterior axis specification;0.031311569005268;16825!GO:0021697;cerebellar cortex formation;0.031311569005268;16825!GO:0021533;cell differentiation in hindbrain;0.031311569005268;16825!GO:0021680;cerebellar Purkinje cell layer development;0.0329351728611453;16825!GO:0021696;cerebellar cortex morphogenesis;0.0329351728611453;16825!GO:0021587;cerebellum morphogenesis;0.0329351728611453;16825!GO:0021575;hindbrain morphogenesis;0.0329351728611453;16825!GO:0009798;axis specification;0.0329351728611453;16825!GO:0021695;cerebellar cortex development;0.0329351728611453;16825!GO:0045638;negative regulation of myeloid cell differentiation;0.0329351728611453;16825!GO:0008373;sialyltransferase activity;0.0329351728611453;20449!GO:0022037;metencephalon development;0.0339951706826381;16825!GO:0021549;cerebellum development;0.0339951706826381;16825!GO:0030173;integral to Golgi membrane;0.0339951706826381;20449!GO:0031228;intrinsic to Golgi membrane;0.0339951706826381;20449!GO:0001702;gastrulation with mouth forming second;0.040377673861967;16825!GO:0045637;regulation of myeloid cell differentiation;0.0437497994423553;16825!GO:0030218;erythrocyte differentiation;0.0444636384954912;16825!GO:0030902;hindbrain development;0.0485829209071958;16825!
|ontology_enrichment_celltype=CL:0000117!3.25e-10!23;CL:0000337!3.25e-10!23;CL:0000540!1.80e-07!33;CL:0000047!1.80e-07!33;CL:0000031!1.80e-07!33;CL:0000404!1.80e-07!33
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!9.51e-20!64;UBERON:0003075!9.51e-20!64;UBERON:0007284!9.51e-20!64;UBERON:0000073!1.22e-19!54;UBERON:0001049!1.56e-18!52;UBERON:0005068!1.56e-18!52;UBERON:0006241!1.56e-18!52;UBERON:0007135!1.56e-18!52;UBERON:0001017!7.29e-17!73;UBERON:0010371!1.16e-16!73;UBERON:0000955!1.96e-16!47;UBERON:0006238!1.96e-16!47;UBERON:0002616!6.55e-16!46;UBERON:0003056!8.55e-16!49;UBERON:0001016!2.13e-15!75;UBERON:0003080!4.22e-14!40;UBERON:0004121!5.00e-14!95;UBERON:0000924!5.00e-14!95;UBERON:0006601!5.00e-14!95;UBERON:0002020!6.74e-14!34;UBERON:0002780!1.75e-13!39;UBERON:0001890!1.75e-13!39;UBERON:0006240!1.75e-13!39;UBERON:0010314!1.03e-12!92;UBERON:0003528!5.61e-12!29;UBERON:0002791!5.61e-12!29;UBERON:0001893!5.61e-12!29;UBERON:0007811!4.18e-09!36;UBERON:0003408!2.56e-08!24;UBERON:0002370!3.19e-08!23;UBERON:0000974!3.19e-08!23;UBERON:0004807!3.19e-08!23;UBERON:0005058!3.19e-08!23;UBERON:0003351!3.19e-08!23;UBERON:0009113!3.19e-08!23;UBERON:0003295!3.19e-08!23;UBERON:0009722!3.19e-08!23;UBERON:0005562!3.19e-08!23;UBERON:0007690!3.19e-08!23;UBERON:0000956!3.95e-08!21;UBERON:0001869!3.95e-08!21;UBERON:0000203!3.95e-08!21;UBERON:0004177!1.45e-07!29;UBERON:0005057!1.45e-07!29;UBERON:0000153!1.61e-07!43;UBERON:0006562!2.82e-07!24;UBERON:0001557!2.82e-07!24;UBERON:0001042!2.82e-07!24;UBERON:0008814!2.82e-07!24;UBERON:0009145!2.82e-07!24;UBERON:0002619!9.32e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.706384,0.330161,0.394491,0.227651,0.40827,0.495658,0.146465,0.468136,0.573183,0.453212,0.484001,1.41744,0.507558,0.24249,0,1.66303,1.17871,0.419123,0.528436,0.296085,0.179861,0.50668,0.64218,0.337218,1.32254,1.30297,1.09532,0.739731,0.0963992,0.414842,0.796599,0.624261,0.735537,0.681042,0.281474,1.1396,0.480503,0.559915,0.500908,0.224094,0.419787,0.0422275,0.244285,0.317317,1.76925,0.618203,0.443479,0.0330279,0.271021,0.679429,0.560572,0.633942,0.937018,0.954342,0.514504,0.279148,1.18878,0.12126,1.27615,1.8289,0.569793,0.163832,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.840217,0.151245,1.14319,0.987652,1.22652,0.710896,0.735293,0.607043,0.759798,0.299972,0.90463,0.713779,0.568383,0.14134,0.873141,3.86213,1.05171,0.0965007,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,1.66008,0.17334,0.14449,0.812053,0.618454,0.0816605,0.210602,0.796322,0.919715,0.680015,0.678976,1.07585,0.737915,0.439611,0.821842,0.297733,0.348012,0.921485,0.301014,0.458194,1.16629,0.222515,1.57752,0.398075,0.697928,0.207304,0.993019,0.647706,1.3263,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.663857,0.90286,1.00644,1.05894,0.527782,1.18781,1.08745,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.956381,1.88479,1.10522,3.07793,0.938577,0.527659,0.526881,1.01974,0.561556,0.253271,0.352329,0.950885,1.1483,0.872292,0.763895,0.914544,0.669337,0.519673,0.209556,0.482466,1.70115
|tfbs_overrepresentation_jaspar=MA0003.1;3.05869,MA0004.1;1.02263,MA0006.1;2.71192,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;4.13225,MA0017.1;0.26239,MA0019.1;0.642876,MA0024.1;0.779446,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;0.692501,MA0029.1;0.757957,MA0030.1;1.80346,MA0031.1;1.73076,MA0038.1;0.534262,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.589612,MA0050.1;0.431976,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;1.02213,MA0056.1;0,MA0057.1;0.549903,MA0058.1;0.305206,MA0059.1;0.316585,MA0060.1;0.169058,MA0061.1;0.56663,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;0.266547,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;0.0771206,MA0074.1;0.488775,MA0076.1;0.279739,MA0077.1;0.804033,MA0078.1;0.575205,MA0081.1;0.897217,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;0.728131,MA0089.1;0,MA0090.1;0.362551,MA0091.1;0.407455,MA0092.1;0.362847,MA0093.1;0.709711,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;0.324888,MA0103.1;0.272167,MA0105.1;0.109964,MA0106.1;0.582805,MA0107.1;0.266586,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;0.555251,MA0114.1;0.19245,MA0115.1;0.921497,MA0116.1;0.670446,MA0117.1;0.88947,MA0119.1;0.325434,MA0122.1;0.909168,MA0124.1;1.11203,MA0125.1;1.03833,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.441109,MA0140.1;0.477483,MA0141.1;0.29014,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;1.07908,MA0145.1;0.442138,MA0146.1;1.46813,MA0147.1;0.593505,MA0148.1;0.410398,MA0149.1;1.58098,MA0062.2;1.7688,MA0035.2;0.482026,MA0039.2;0.618828,MA0138.2;0.630612,MA0002.2;0.145685,MA0137.2;0.783415,MA0104.2;0.157347,MA0047.2;0.533516,MA0112.2;0.442124,MA0065.2;0.200864,MA0150.1;0.380623,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.0809407,MA0155.1;0.845235,MA0156.1;0.278949,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.214506,MA0160.1;0.413266,MA0161.1;0,MA0162.1;1.61761,MA0163.1;0.321031,MA0164.1;0.508398,MA0080.2;0.267388,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;1.74198,MA0102.2;1.5442,MA0258.1;0.533988,MA0259.1;1.08444,MA0442.1;0
}}

Latest revision as of 15:56, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:70205025..70205099,-p4@Rhobtb2
Mm9::chr15:63891780..63891840,-p4@Fam49b
Mm9::chr19:46119482..46119617,-p1@Ldb1
Mm9::chr1:181476539..181476564,+p2@Cnst
Mm9::chr6:142912628..142912648,-p5@St8sia1
Mm9::chr6:142912655..142912712,-p1@St8sia1
Mm9::chr6:142912888..142912923,-p2@St8sia1
Mm9::chr6:142912924..142912958,-p4@St8sia1
Mm9::chr7:25689435..25689478,+p2@Arhgef1


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:0030274LIM domain binding0.031311569005268
GO:0045647negative regulation of erythrocyte differentiation0.031311569005268
GO:0003828alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity0.031311569005268
GO:0021692cerebellar Purkinje cell layer morphogenesis0.031311569005268
GO:0045646regulation of erythrocyte differentiation0.031311569005268
GO:0021694cerebellar Purkinje cell layer formation0.031311569005268
GO:0021702cerebellar Purkinje cell differentiation0.031311569005268
GO:0007264small GTPase mediated signal transduction0.031311569005268
GO:0009948anterior/posterior axis specification0.031311569005268
GO:0021697cerebellar cortex formation0.031311569005268
GO:0021533cell differentiation in hindbrain0.031311569005268
GO:0021680cerebellar Purkinje cell layer development0.0329351728611453
GO:0021696cerebellar cortex morphogenesis0.0329351728611453
GO:0021587cerebellum morphogenesis0.0329351728611453
GO:0021575hindbrain morphogenesis0.0329351728611453
GO:0009798axis specification0.0329351728611453
GO:0021695cerebellar cortex development0.0329351728611453
GO:0045638negative regulation of myeloid cell differentiation0.0329351728611453
GO:0008373sialyltransferase activity0.0329351728611453
GO:0022037metencephalon development0.0339951706826381
GO:0021549cerebellum development0.0339951706826381
GO:0030173integral to Golgi membrane0.0339951706826381
GO:0031228intrinsic to Golgi membrane0.0339951706826381
GO:0001702gastrulation with mouth forming second0.040377673861967
GO:0045637regulation of myeloid cell differentiation0.0437497994423553
GO:0030218erythrocyte differentiation0.0444636384954912
GO:0030902hindbrain development0.0485829209071958



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
CNS neuron (sensu Vertebrata)3.25e-1023
neuroblast (sensu Vertebrata)3.25e-1023
neuron1.80e-0733
neuronal stem cell1.80e-0733
neuroblast1.80e-0733
electrically signaling cell1.80e-0733

Uber Anatomy
Ontology termp-valuen
neurectoderm9.51e-2064
neural plate9.51e-2064
presumptive neural plate9.51e-2064
regional part of nervous system1.22e-1954
neural tube1.56e-1852
neural rod1.56e-1852
future spinal cord1.56e-1852
neural keel1.56e-1852
central nervous system7.29e-1773
ecto-epithelium1.16e-1673
brain1.96e-1647
future brain1.96e-1647
regional part of brain6.55e-1646
pre-chordal neural plate8.55e-1649
nervous system2.13e-1575
anterior neural tube4.22e-1440
ectoderm-derived structure5.00e-1495
ectoderm5.00e-1495
presumptive ectoderm5.00e-1495
gray matter6.74e-1434
regional part of forebrain1.75e-1339
forebrain1.75e-1339
future forebrain1.75e-1339
structure with developmental contribution from neural crest1.03e-1292
brain grey matter5.61e-1229
regional part of telencephalon5.61e-1229
telencephalon5.61e-1229
craniocervical region4.18e-0936
gland of gut2.56e-0824
thymus3.19e-0823
neck3.19e-0823
respiratory system epithelium3.19e-0823
hemolymphoid system gland3.19e-0823
pharyngeal epithelium3.19e-0823
thymic region3.19e-0823
pharyngeal gland3.19e-0823
entire pharyngeal arch endoderm3.19e-0823
thymus primordium3.19e-0823
early pharyngeal endoderm3.19e-0823
cerebral cortex3.95e-0821
cerebral hemisphere3.95e-0821
pallium3.95e-0821
hemopoietic organ1.45e-0729
immune organ1.45e-0729
anterior region of body1.61e-0743
pharynx2.82e-0724
upper respiratory tract2.82e-0724
chordate pharynx2.82e-0724
pharyngeal arch system2.82e-0724
pharyngeal region of foregut2.82e-0724
regional part of cerebral cortex9.32e-0717


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)
MA0003.13.05869
MA0004.11.02263
MA0006.12.71192
MA0007.10.38073
MA0009.10.82278
MA0014.14.13225
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.692501
MA0029.10.757957
MA0030.11.80346
MA0031.11.73076
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.589612
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.11.02213
MA0056.10
MA0057.10.549903
MA0058.10.305206
MA0059.10.316585
MA0060.10.169058
MA0061.10.56663
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.266547
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.0771206
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.897217
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.728131
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.709711
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.272167
MA0105.10.109964
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.19245
MA0115.10.921497
MA0116.10.670446
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.441109
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.11.07908
MA0145.10.442138
MA0146.11.46813
MA0147.10.593505
MA0148.10.410398
MA0149.11.58098
MA0062.21.7688
MA0035.20.482026
MA0039.20.618828
MA0138.20.630612
MA0002.20.145685
MA0137.20.783415
MA0104.20.157347
MA0047.20.533516
MA0112.20.442124
MA0065.20.200864
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.0809407
MA0155.10.845235
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.11.61761
MA0163.10.321031
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.21.74198
MA0102.21.5442
MA0258.10.533988
MA0259.11.08444
MA0442.10
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