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MCL coexpression mm9:199: Difference between revisions

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{{MCL_coexpression_mm9
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vesicle targeting;0.00788911411822714;192167!GO:0006903;vesicle targeting;0.00788911411822714;192167!GO:0042043;neurexin binding;0.00788911411822714;192167!GO:0016079;synaptic vesicle exocytosis;0.00788911411822714;192167!GO:0051650;establishment of vesicle localization;0.00788911411822714;192167!GO:0051648;vesicle localization;0.00788911411822714;192167!GO:0007416;synaptogenesis;0.0096820945996424;192167!GO:0051656;establishment of organelle localization;0.0096820945996424;192167!GO:0048489;synaptic vesicle transport;0.0096820945996424;192167!GO:0051640;organelle localization;0.0096820945996424;192167!GO:0045664;regulation of neuron differentiation;0.0096820945996424;192167!GO:0050808;synapse organization and biogenesis;0.0144633758834164;192167!GO:0007269;neurotransmitter secretion;0.0154748007703686;192167!GO:0045055;regulated secretory pathway;0.018032260841662;192167!GO:0006887;exocytosis;0.0204188836001173;192167!GO:0003001;generation of a signal involved in cell-cell signaling;0.0204188836001173;192167!GO:0001505;regulation of neurotransmitter levels;0.0204188836001173;192167!GO:0043062;extracellular structure organization and biogenesis;0.0216950638251246;192167!GO:0045211;postsynaptic membrane;0.0226293010233357;192167!GO:0044456;synapse part;0.0238645702076371;192167!GO:0045595;regulation of cell differentiation;0.0287389157163989;192167!GO:0045045;secretory pathway;0.0301844366262604;192167!GO:0007017;microtubule-based process;0.0301844366262604;192167!GO:0007268;synaptic transmission;0.0312277433846491;192167!GO:0032940;secretion by cell;0.0325031501670958;192167!GO:0019226;transmission of nerve impulse;0.0341355899346367;192167!GO:0050793;regulation of developmental process;0.0364871527968005;192167!GO:0046903;secretion;0.0364871527968005;192167!GO:0030182;neuron differentiation;0.0376773208749814;192167!GO:0048699;generation of neurons;0.0413542272326423;192167!GO:0007267;cell-cell signaling;0.0413542272326423;192167!GO:0022008;neurogenesis;0.0416643839368871;192167!GO:0030054;cell junction;0.0457807682921363;192167!GO:0016192;vesicle-mediated 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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0682179984609265,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0818436986734574,0,0,0,0,0,0,0,0,0.0987733636723519,0.164596587144155,0,0.0380188235580625,0,0,0,0.20714756397787,0.275054562543737,0.155369784735907,0.0742309351586685,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0482820047261801,0,0,0,0,0,0,0,0,0.20018311764962,0.151949772756791,0,0,0,0,0.161179842546876,0.28216905172576,0.0514050548005424,0.229245865416417,0.35766376392443,0.150933218241173,0.257967923814717,0.0805105854221362,0,0,0.0829439327499637,0.181981218013818,0,0.133578586898209,0.448467904704167,0.492639087141722,0.596224824531674,0.36395479503125,0.181102009199648,0,0,0,0,0.106546909924599,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.212419302822567,0.149717325850531,0,0,0,0.0906941294286938,0,0,0,0,0,0,0,0,0,0,0,0,0,0.046982063026719,0,0,0,0.0294389011296462,0.0266298923127834,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.120936080462619,0.130859448321889,0,0,0,0,0,0,0,0,0,0,0,0.215543090236368,0,0,0,0.0663147875126409,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0719044921483595,0,0,0,0.0712812415377886,0.0661577744756082,0,0,0,0,0,0,0,0,0,0,0.136990127740213,0,0,0,0,0,0,0,0,0,0,0,0,0.0445418537893845,0,0,0,0,0,0,0,0,0,0,0,0.0123675556853881,0.126427630498926,0.0915665403705771,0.0531569878936061,0,0,0,0,0,0.0424616899933645,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.582490536396736,0.518727899922476,0.58709079061676,0.486038968127383,0.374778587894724,0.514040340140897,0.480735069848811,0.447357266760456,0.449103283876296,0.407098602473158,0,0,0,0.0945084131504676,0,0,0.0871588832444397,0.081359932135904,0,0,0,0,0.0745542549075041,0.0523284672130554,0.0472245945615809,0,0.0476191773904887,0.0766073954291401,0,0.0596387295197733,0.128033729919821,0.131923786075207,0.092873634605593,0.0589368614163519,0.0390607415003592,0.0678996586311492,0.0729583017401753,0.101427320830301,0.104353329269123,0,0.0486884105045233,0.0780974029773103,0,0.0625582350728301,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0016080;synaptic vesicle targeting;0.00788911411822714;192167!GO:0006903;vesicle targeting;0.00788911411822714;192167!GO:0042043;neurexin binding;0.00788911411822714;192167!GO:0016079;synaptic vesicle exocytosis;0.00788911411822714;192167!GO:0051650;establishment of vesicle localization;0.00788911411822714;192167!GO:0051648;vesicle localization;0.00788911411822714;192167!GO:0007416;synaptogenesis;0.0096820945996424;192167!GO:0051656;establishment of organelle localization;0.0096820945996424;192167!GO:0048489;synaptic vesicle transport;0.0096820945996424;192167!GO:0051640;organelle localization;0.0096820945996424;192167!GO:0045664;regulation of neuron differentiation;0.0096820945996424;192167!GO:0050808;synapse organization and biogenesis;0.0144633758834164;192167!GO:0007269;neurotransmitter secretion;0.0154748007703686;192167!GO:0045055;regulated secretory pathway;0.018032260841662;192167!GO:0006887;exocytosis;0.0204188836001173;192167!GO:0003001;generation of a signal involved in cell-cell signaling;0.0204188836001173;192167!GO:0001505;regulation of neurotransmitter levels;0.0204188836001173;192167!GO:0043062;extracellular structure organization and biogenesis;0.0216950638251246;192167!GO:0045211;postsynaptic membrane;0.0226293010233357;192167!GO:0044456;synapse part;0.0238645702076371;192167!GO:0045595;regulation of cell differentiation;0.0287389157163989;192167!GO:0045045;secretory pathway;0.0301844366262604;192167!GO:0007017;microtubule-based process;0.0301844366262604;192167!GO:0007268;synaptic transmission;0.0312277433846491;192167!GO:0032940;secretion by cell;0.0325031501670958;192167!GO:0019226;transmission of nerve impulse;0.0341355899346367;192167!GO:0050793;regulation of developmental process;0.0364871527968005;192167!GO:0046903;secretion;0.0364871527968005;192167!GO:0030182;neuron differentiation;0.0376773208749814;192167!GO:0048699;generation of neurons;0.0413542272326423;192167!GO:0007267;cell-cell signaling;0.0413542272326423;192167!GO:0022008;neurogenesis;0.0416643839368871;192167!GO:0030054;cell junction;0.0457807682921363;192167!GO:0016192;vesicle-mediated transport;0.0465225700207218;192167!
}}

Latest revision as of 14:52, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:28935822..28935827,+p@chr10:28935822..28935827
+
Mm9::chr16:74754890..74754894,-p@chr16:74754890..74754894
-
Mm9::chr16:74829090..74829095,-p@chr16:74829090..74829095
-
Mm9::chr16:74961384..74961388,-p@chr16:74961384..74961388
-
Mm9::chr16:75016670..75016679,-p@chr16:75016670..75016679
-
Mm9::chr16:75052435..75052441,-p@chr16:75052435..75052441
-
Mm9::chr18:40415943..40415963,+p@chr18:40415943..40415963
+
Mm9::chr18:71901216..71901226,-p@chr18:71901216..71901226
-
Mm9::chr18:72318744..72318754,-p@chr18:72318744..72318754
-
Mm9::chr18:77736935..77736948,-p@chr18:77736935..77736948
-
Mm9::chr18:77769901..77769933,-p@chr18:77769901..77769933
-
Mm9::chr19:19011087..19011096,-p@chr19:19011087..19011096
-
Mm9::chr19:50694706..50694712,-p@chr19:50694706..50694712
-
Mm9::chr1:38888222..38888234,-p@chr1:38888222..38888234
-
Mm9::chr3:25435716..25435717,-p@chr3:25435716..25435717
-
Mm9::chr3:25489312..25489320,-p@chr3:25489312..25489320
-
Mm9::chr3:25571575..25571580,-p@chr3:25571575..25571580
-
Mm9::chr3:25584256..25584277,-p@chr3:25584256..25584277
-
Mm9::chr3:25597053..25597061,-p@chr3:25597053..25597061
-
Mm9::chr3:25603987..25603995,-p@chr3:25603987..25603995
-
Mm9::chr3:25642170..25642173,-p@chr3:25642170..25642173
-
Mm9::chr3:25689319..25689331,-p@chr3:25689319..25689331
-
Mm9::chr3:25689516..25689560,-p@chr3:25689516..25689560
-
Mm9::chr3:25717760..25717764,-p@chr3:25717760..25717764
-
Mm9::chr3:25723293..25723296,-p@chr3:25723293..25723296
-
Mm9::chr3:25734220..25734224,-p@chr3:25734220..25734224
-
Mm9::chr3:25737370..25737385,-p@chr3:25737370..25737385
-
Mm9::chr3:25746253..25746268,-p@chr3:25746253..25746268
-
Mm9::chr3:25746283..25746292,-p@chr3:25746283..25746292
-
Mm9::chr3:25756325..25756329,-p@chr3:25756325..25756329
-
Mm9::chr3:25767628..25767676,-p@chr3:25767628..25767676
-
Mm9::chr3:25926009..25926021,-p@chr3:25926009..25926021
-
Mm9::chr3:25926051..25926062,-p@chr3:25926051..25926062
-
Mm9::chr3:25926177..25926188,-p@chr3:25926177..25926188
-
Mm9::chr3:25926203..25926216,-p@chr3:25926203..25926216
-
Mm9::chr3:25926282..25926291,-p@chr3:25926282..25926291
-
Mm9::chr3:25926321..25926332,-p@chr3:25926321..25926332
-
Mm9::chr3:25944957..25944973,-p@chr3:25944957..25944973
-
Mm9::chr3:25945015..25945031,-p@chr3:25945015..25945031
-
Mm9::chr3:25945353..25945362,-p@chr3:25945353..25945362
-
Mm9::chr3:25958354..25958359,-p@chr3:25958354..25958359
-
Mm9::chr3:26018333..26018354,-p@chr3:26018333..26018354
-
Mm9::chr3:26216750..26216752,-p@chr3:26216750..26216752
-
Mm9::chr3:26230728..26230742,-p8@Nlgn1
Mm9::chr5:100046932..100046936,-p@chr5:100046932..100046936
-
Mm9::chr6:110599092..110599106,+p@chr6:110599092..110599106
+
Mm9::chr7:131161662..131161668,+p@chr7:131161662..131161668
+


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:0016080synaptic vesicle targeting0.00788911411822714
GO:0006903vesicle targeting0.00788911411822714
GO:0042043neurexin binding0.00788911411822714
GO:0016079synaptic vesicle exocytosis0.00788911411822714
GO:0051650establishment of vesicle localization0.00788911411822714
GO:0051648vesicle localization0.00788911411822714
GO:0007416synaptogenesis0.0096820945996424
GO:0051656establishment of organelle localization0.0096820945996424
GO:0048489synaptic vesicle transport0.0096820945996424
GO:0051640organelle localization0.0096820945996424
GO:0045664regulation of neuron differentiation0.0096820945996424
GO:0050808synapse organization and biogenesis0.0144633758834164
GO:0007269neurotransmitter secretion0.0154748007703686
GO:0045055regulated secretory pathway0.018032260841662
GO:0006887exocytosis0.0204188836001173
GO:0003001generation of a signal involved in cell-cell signaling0.0204188836001173
GO:0001505regulation of neurotransmitter levels0.0204188836001173
GO:0043062extracellular structure organization and biogenesis0.0216950638251246
GO:0045211postsynaptic membrane0.0226293010233357
GO:0044456synapse part0.0238645702076371
GO:0045595regulation of cell differentiation0.0287389157163989
GO:0045045secretory pathway0.0301844366262604
GO:0007017microtubule-based process0.0301844366262604
GO:0007268synaptic transmission0.0312277433846491
GO:0032940secretion by cell0.0325031501670958
GO:0019226transmission of nerve impulse0.0341355899346367
GO:0050793regulation of developmental process0.0364871527968005
GO:0046903secretion0.0364871527968005
GO:0030182neuron differentiation0.0376773208749814
GO:0048699generation of neurons0.0413542272326423
GO:0007267cell-cell signaling0.0413542272326423
GO:0022008neurogenesis0.0416643839368871
GO:0030054cell junction0.0457807682921363
GO:0016192vesicle-mediated transport0.0465225700207218



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
neurectoderm9.75e-2464
neural plate9.75e-2464
presumptive neural plate9.75e-2464
pre-chordal neural plate2.20e-2049
ecto-epithelium3.23e-1973
regional part of nervous system3.11e-1854
neural tube6.52e-1852
neural rod6.52e-1852
future spinal cord6.52e-1852
neural keel6.52e-1852
brain1.81e-1647
future brain1.81e-1647
regional part of brain1.63e-1546
ectoderm-derived structure7.79e-1595
ectoderm7.79e-1595
presumptive ectoderm7.79e-1595
occipital lobe1.92e-1410
visual cortex1.92e-1410
neocortex1.92e-1410
structure with developmental contribution from neural crest1.82e-1392
anterior neural tube3.77e-1340
central nervous system7.12e-1373
gray matter1.26e-1234
regional part of forebrain2.73e-1239
forebrain2.73e-1239
future forebrain2.73e-1239
nervous system3.01e-1275
brain grey matter2.98e-1129
regional part of telencephalon2.98e-1129
telencephalon2.98e-1129
cerebral cortex9.30e-1121
cerebral hemisphere9.30e-1121
pallium9.30e-1121
regional part of cerebral cortex1.60e-1017
eye3.97e-099
camera-type eye3.97e-099
simple eye3.97e-099
immature eye3.97e-099
ocular region3.97e-099
visual system3.97e-099
face3.97e-099
optic cup3.97e-099
optic vesicle3.97e-099
eye primordium3.97e-099
subdivision of head4.23e-0711


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)
MA0003.12.2673e-11
MA0004.10.297268
MA0006.10.00486362
MA0007.10.273273
MA0009.10.241801
MA0014.19.40856e-08
MA0017.10.228067
MA0019.10.130554
MA0024.10.212626
MA0025.11.0712
MA0027.11.75175
MA0028.10.00565061
MA0029.11.09322
MA0030.11.10962
MA0031.10.533273
MA0038.10.268681
MA0040.11.29152
MA0041.11.66274
MA0042.10.847744
MA0043.10.310854
MA0046.11.35234
MA0048.14.55281e-05
MA0050.10.363193
MA0051.10.0817759
MA0052.10.711293
MA0055.15.8208e-06
MA0056.10
MA0057.10.0162665
MA0058.10.15995
MA0059.10.0667434
MA0060.10.00821251
MA0061.10.00212643
MA0063.10
MA0066.10.0735644
MA0067.10.509729
MA0068.10.0408783
MA0069.10.711839
MA0070.10.249498
MA0071.10.361715
MA0072.10.243673
MA0073.11.11748
MA0074.10.0599302
MA0076.10.00898052
MA0077.10.648574
MA0078.10.096354
MA0081.10.0179065
MA0083.10.310264
MA0084.10.803542
MA0087.11.39657
MA0088.10.00420932
MA0089.10
MA0090.10.0228278
MA0091.10.135958
MA0092.10.244225
MA0093.10.100028
MA0095.10
MA0098.10
MA0100.10.0558545
MA0101.10.0155449
MA0103.10.0420093
MA0105.10.000174411
MA0106.10.0999571
MA0107.10.00748335
MA0108.20.440045
MA0109.10
MA0111.10.0258231
MA0113.10.0871934
MA0114.10.10652
MA0115.10.312936
MA0116.10.0273676
MA0117.10.289199
MA0119.10.0724076
MA0122.10.303728
MA0124.10.464833
MA0125.11.0427
MA0130.10
MA0131.10.128156
MA0132.10
MA0133.10
MA0135.11.61024
MA0136.10.067305
MA0139.10.0173564
MA0140.10.204612
MA0141.10.140497
MA0142.10.171883
MA0143.10.313939
MA0144.10.110364
MA0145.10.000453348
MA0146.10.000582319
MA0147.10.0165912
MA0148.10.324184
MA0149.10.0164376
MA0062.20.00020539
MA0035.21.21495
MA0039.21.45347e-11
MA0138.20.12401
MA0002.20.10653
MA0137.20.280643
MA0104.20.00628566
MA0047.20.565868
MA0112.20.000453257
MA0065.20.0150824
MA0150.10.113044
MA0151.10
MA0152.10.56609
MA0153.10.926017
MA0154.10.0887053
MA0155.10.000144952
MA0156.10.00888551
MA0157.10.153179
MA0158.10
MA0159.10.263263
MA0160.10.597227
MA0161.10
MA0162.11.36819e-07
MA0163.16.85787e-07
MA0164.10.0674435
MA0080.20.00756959
MA0018.20.0712081
MA0099.20.383444
MA0079.21.92865e-16
MA0102.20.852517
MA0258.10.010524
MA0259.10.0141218
MA0442.10
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