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MCL coexpression mm9:1119: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=0.0990693774849063,0,0,0,0,0.0096282786338559,0.0260510888180396,0,0,0.0130482669320792,0,0,0,0,0,0,0,0,0.00797202459262621,0,0.220221078352499,0,0,0,0.0128137839109815,0,0,0.0121063835118862,0,0,0,0,0,0,0.015743274524663,0,0,0,0,0,0,0,0,0.0139332484705757,0,0,0,0.0122366082934508,0.0349173234753411,0.0285086265338436,0.0153143936381474,0,0,0,0,0,0,0,0.458272311562779,0.607719031954419,0.432334105621554,0,0,0,0,0,0.0722998254415377,0.189040114522218,0.149324701642968,0.200914254352537,0.174275840044673,0.647074475610048,0.644825580886425,0.452141417536811,0.406390411422135,0.339795194368955,0.36881920654442,0.391968772180522,0.423359477480212,0.486698374512263,0.593530129268896,0.566414377723627,0.323086179391508,0.35872785851991,0.452341918367097,0.863855998451428,0.867501436037657,0.581676267035115,0.00452882051177816,0.0171975532606965,0,0,0,0,0,0,0.0565145416273034,0,0,0,0.180149876460348,0,0,0,0,0,0,0.0182758570219281,0,0.0247157635472197,0.0468848473218454,0.0459957140168159,0.0364058936366868,0.0231452627108806,0.0678365215290768,0.0212546768745505,0,0,0,0.0469803066110183,0.0123798986254107,0,0,0.221095839893875,0.216071737165126,0.0141145516584203,0,0,0,0.536522650330725,0.832566980036145,0.974526622685822,0.541817369746443,0.525704752637104,0.595632286354837,0.663820623920548,0.073517720883531,0.0145495797983134,0.0139792810569848,0.109498501814914,0.07364764252338,0.10295643730456,0.0959830490767439,0.135719205376028,0.193136107231386,0.238127414326005,0.230366377424668,0.210469148069091,0.0453731564467106,0.0493711982118078,0.059859555170716,0.0348500758863445,0.0692839625406469,0.0625643372693978,0.118581247458563,0.0320514365693583,0,0,0,0,0.013071466002467,0.0190826490361187,0.0131828671988084,0.0111440858217073,0,0,0,0.00685170394538421,0,0,0,0,0,0,0.598984410107839,0.50644498195773,0,0.0145574079132351,0.0220421522764077,0.0366250857870393,0.0217474392675219,0.0324230545859262,0.0228277904435987,0.0108041852274402,0,0.0189181959164371,0.0139105234964038,0.0112576309114779,0.0314781730979075,0,0,0.0112671930318192,0.0215502125196958,0.0377642700035241,0.0936523669841528,0,0.0219962984493358,0.0415061800465706,0.00380427033039763,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0107659015344827,0.0175029402106981,0.025536706032012,0,0.0179264767073001,0.0132479933972821,0.0110594962458164,0,0,0,0.00941456847508854,0.00988305190599354,0,0,0,0,0,0.425440041862024,0.44217782914989,0,0.025359960094655,0.017013366563148,0.0204502658288287,0.0787867140205278,0.0663077344801689,0.0228639061249091,0.0278334576849779,0.042176516279,0.0636277197370834,0.0413325114388374,0.392163946590626,0.0278970962902314,0.0367215073759084,0.0841710706235519,0.00947354107323442,0,0.0380407209926317,0.0857774927630793,0.0214393091359241,0.0448475731360677,0.016631450854307,0,0.0192379836387817,0.0189169941093429,0,0,0,0.181052517424017,0.0795343538841666,0.0842765235828907,0.128088072466684,0.174118530178636,0.203978531543403,0.230081797874651,0.217514465109943,0,0.0567332299781659,0,0,0.11036440405673,0.0753162547091097,0.0826617822964001,0.0424545811061729,0.0284957714045469,0.375266707430935,0,0,0.010541376779981,0,0,0,0,0,0.0273022132963274,0,0.0462429723646903,0.0211689477211694,0.0127262439398241,0.0570149092021164,0.0245075845997983,0.00784913602242114,0,0.0144250512332046,0.00756149148765094,0,0.131505877753237,0.0581699319223983,0.0367349409070276,0.0505592454228537,0.0226094644977611,0.0277465487946478,0.0199655124609838,0.0151877108267446,0.0179987690273055,0.0759908216318829,0.108415179323607,0,0,0.00606595571333779,0.00757828745735574,0,0.0320018427698492,0.00704197201952887,0.0256390365694045,0.00596772639983224,0,0,0.0057696944965792,0.00569921273616349,0,0.0126784459996771,0.0124380305366603,0.0053303533349064,0,0,0,0,0,0.0252208844907596,0.30586051632833,0.304768152770844,0.381671716839072,0.287071227834201,0.306343214688053,0.391939130805018,0.38307734195762,0.355251662438635,0.316329781995656,0.392935098697662,0.0863813853128339,0.13725341536301,0.135985586266082,0.189605407740801,0.220234590147897,0.227228738768119,0.237901059505839,0.258563181862895,0.286745226381307,0.288634490553602,0.221732978149563,0.235124479695897,0.222629554516039,0.29228608106447,0.292405742681283,0.331251888093341,0.223689625337088,0.259377185960179,0.32035532265565,0.295705519127697,0.282278200837277,0.221119660768012,0.263690281107044,0.25912002863516,0.285300744223224,0.231560419992001,0.242265041078137,0.207215658478798,0.310506367830326,0.174977943431159,0.258748003165744,0.217341491458242,0.148774383220205,0.2131578615973,0.249807432088865,0.353379534801425,0.187366756052484,0.233951897860696,0.145142942543808,0.136467751181536,0.0736355851631309|coexpression_dpi_cluster_scores_median=0.064513712786576,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.127160916153114,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.450379707787695,0.62054681318495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activating metabotropic glutamate receptor activity;0.036972118507159;108071!GO:0047631;ADP-ribose diphosphatase 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|ontology_enrichment_celltype=CL:0000117!6.15e-21!23;CL:0000337!6.15e-21!23;CL:0000540!6.71e-15!33;CL:0000047!6.71e-15!33;CL:0000031!6.71e-15!33;CL:0000404!6.71e-15!33;CL:0000393!3.31e-11!39;CL:0000211!3.31e-11!39;CL:0000221!1.23e-09!44;CL:0000133!1.23e-09!44;CL:0002319!2.31e-09!43;CL:0000055!3.18e-07!49
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.58e-32!54;UBERON:0002346!1.94e-32!64;UBERON:0003075!1.94e-32!64;UBERON:0007284!1.94e-32!64;UBERON:0001049!1.14e-30!52;UBERON:0005068!1.14e-30!52;UBERON:0006241!1.14e-30!52;UBERON:0007135!1.14e-30!52;UBERON:0001017!7.83e-30!73;UBERON:0001016!1.67e-28!75;UBERON:0010371!4.69e-28!73;UBERON:0004121!9.74e-27!95;UBERON:0000924!9.74e-27!95;UBERON:0006601!9.74e-27!95;UBERON:0002020!2.66e-26!34;UBERON:0003056!5.29e-26!49;UBERON:0000955!2.48e-25!47;UBERON:0006238!2.48e-25!47;UBERON:0002616!2.12e-24!46;UBERON:0003080!3.21e-23!40;UBERON:0002780!3.62e-22!39;UBERON:0001890!3.62e-22!39;UBERON:0006240!3.62e-22!39;UBERON:0003528!6.15e-21!29;UBERON:0002791!6.15e-21!29;UBERON:0001893!6.15e-21!29;UBERON:0010314!4.62e-19!92;UBERON:0000956!2.44e-13!21;UBERON:0001869!2.44e-13!21;UBERON:0000203!2.44e-13!21;UBERON:0002619!3.37e-11!17;UBERON:0002420!5.15e-09!8;UBERON:0007245!5.15e-09!8;UBERON:0010009!5.15e-09!8;UBERON:0010011!5.15e-09!8;UBERON:0000454!5.15e-09!8;UBERON:0002021!7.03e-09!10;UBERON:0000411!7.03e-09!10;UBERON:0001950!7.03e-09!10;UBERON:0003076!8.70e-08!12;UBERON:0003057!8.70e-08!12;UBERON:0002240!1.77e-07!6;UBERON:0005174!1.77e-07!6;UBERON:0001137!1.77e-07!6
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,0.219671,0.542749,0.575086,0.59526,0.599731,0.315771,0,0.795315,0.291368,0.19222,0.361892,0.374752,0.27937,0.598814,0.29769,0.419327,1.51917,0.542568,0.516511,0.344372,0.145661,0.50223,0.897561,0.78719,0.166577,0.316253,0.756613,0.279977,0.57142,0.258564,0.652422,0.295233,0.507468,0.54842,0.317766,0.115244,0.469348,0.714592,0.532496,0.82704,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.608073,0.0869413,1.09164,0.17012,0.482617,0.498755,0.703064,0.859987,1.75229,0.212973,0.812889,0.663039,0.580284,0.975495,0.0369809,2.50868,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.668513,0.203879,0.913319,0.71485,0.127063,0.7665,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.418498,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,5.56098,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,1.54859,0.908128,0.770616,0.507927,0.717753,2.03691,1.13988,0.300961,0.886471,0.256263,1.04192,0.681896,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,1.09603,0.767269,0.612377,0.278874,0.573477,0.0206035
}}

Latest revision as of 16:25, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:56997135..56997154,-p1@Trpc7
Mm9::chr1:16510187..16510214,-p4@Stau2
Mm9::chr4:128798943..128798978,-p2@Hpca
Mm9::chr7:31229598..31229630,-p@chr7:31229598..31229630
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Mm9::chr7:94732627..94732640,+p5@Grm5
Mm9::chr8:111775378..111775391,-p@chr8:111775378..111775391
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Mm9::chrX:22873193..22873235,-p5@Klhl13


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:0001639PLC activating metabotropic glutamate receptor activity0.036972118507159
GO:0047631ADP-ribose diphosphatase activity0.036972118507159



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
regional part of nervous system1.58e-3254
neurectoderm1.94e-3264
neural plate1.94e-3264
presumptive neural plate1.94e-3264
neural tube1.14e-3052
neural rod1.14e-3052
future spinal cord1.14e-3052
neural keel1.14e-3052
central nervous system7.83e-3073
nervous system1.67e-2875
ecto-epithelium4.69e-2873
ectoderm-derived structure9.74e-2795
ectoderm9.74e-2795
presumptive ectoderm9.74e-2795
gray matter2.66e-2634
pre-chordal neural plate5.29e-2649
brain2.48e-2547
future brain2.48e-2547
regional part of brain2.12e-2446
anterior neural tube3.21e-2340
regional part of forebrain3.62e-2239
forebrain3.62e-2239
future forebrain3.62e-2239
brain grey matter6.15e-2129
regional part of telencephalon6.15e-2129
telencephalon6.15e-2129
structure with developmental contribution from neural crest4.62e-1992
cerebral cortex2.44e-1321
cerebral hemisphere2.44e-1321
pallium2.44e-1321
regional part of cerebral cortex3.37e-1117
basal ganglion5.15e-098
nuclear complex of neuraxis5.15e-098
aggregate regional part of brain5.15e-098
collection of basal ganglia5.15e-098
cerebral subcortex5.15e-098
occipital lobe7.03e-0910
visual cortex7.03e-0910
neocortex7.03e-0910
posterior neural tube8.70e-0812
chordal neural plate8.70e-0812
spinal cord1.77e-076
dorsal region element1.77e-076
dorsum1.77e-076


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)
MA0003.10.0286946
MA0004.10.481116
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.10.425579
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.40238
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.362005
MA0056.10
MA0057.10.376102
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.724575
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.385183
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.152496
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.285759
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.11.13539
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.10.677988
MA0107.10.906859
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.836994
MA0117.10.992087
MA0119.11.04809
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.0910975
MA0146.10.108739
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.367001
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.218974
MA0047.20.626803
MA0112.20.0910939
MA0065.20.305574
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.397336
MA0155.10.336768
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.55478
MA0163.10.28052
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.21.96358
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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