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MCL coexpression mm9:2858: Difference between revisions

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{{MCL_coexpression_mm9
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dehydrogenase (quinone) activity;0.0294905635102609;230075!GO:0003954;NADH dehydrogenase activity;0.0294905635102609;230075!GO:0008137;NADH dehydrogenase (ubiquinone) activity;0.0294905635102609;230075!GO:0016655;oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor;0.0294905635102609;230075!GO:0016651;oxidoreductase activity, acting on NADH or 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|ontology_enrichment_celltype=CL:0002319!7.26e-13!43;CL:0000221!1.03e-12!44;CL:0000133!1.03e-12!44;CL:0000055!2.40e-12!49;CL:0000117!2.02e-11!23;CL:0000337!2.02e-11!23;CL:0000540!1.86e-08!33;CL:0000047!1.86e-08!33;CL:0000031!1.86e-08!33;CL:0000404!1.86e-08!33;CL:0000393!4.39e-08!39;CL:0000211!4.39e-08!39;CL:0002321!4.80e-08!70
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!5.33e-20!75;UBERON:0001017!6.26e-20!73;UBERON:0010314!1.28e-19!92;UBERON:0000073!1.00e-17!54;UBERON:0001049!1.53e-16!52;UBERON:0005068!1.53e-16!52;UBERON:0006241!1.53e-16!52;UBERON:0007135!1.53e-16!52;UBERON:0002020!5.40e-16!34;UBERON:0000955!1.09e-13!47;UBERON:0006238!1.09e-13!47;UBERON:0002616!1.39e-13!46;UBERON:0003528!2.13e-13!29;UBERON:0002791!2.13e-13!29;UBERON:0001893!2.13e-13!29;UBERON:0004121!3.44e-13!95;UBERON:0000924!3.44e-13!95;UBERON:0006601!3.44e-13!95;UBERON:0002346!6.64e-13!64;UBERON:0003075!6.64e-13!64;UBERON:0007284!6.64e-13!64;UBERON:0003080!8.68e-11!40;UBERON:0002780!2.14e-10!39;UBERON:0001890!2.14e-10!39;UBERON:0006240!2.14e-10!39;UBERON:0000956!1.02e-09!21;UBERON:0001869!1.02e-09!21;UBERON:0000203!1.02e-09!21;UBERON:0010371!1.30e-09!73;UBERON:0000025!1.67e-09!114;UBERON:0004111!4.48e-09!122;UBERON:0002619!1.27e-08!17;UBERON:0007100!1.11e-07!18;UBERON:0000948!1.11e-07!18;UBERON:0005498!1.11e-07!18;UBERON:0004140!1.11e-07!18;UBERON:0009881!1.11e-07!18;UBERON:0004141!1.11e-07!18;UBERON:0003084!1.11e-07!18;UBERON:0007005!1.11e-07!18;UBERON:0004139!1.11e-07!18;UBERON:0004291!1.11e-07!18;UBERON:0003056!1.28e-07!49;UBERON:0003103!3.17e-07!43;UBERON:0003076!5.64e-07!12;UBERON:0003057!5.64e-07!12
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.564138,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.235304,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.275782,0.932027,1.43154,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.144706,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.474221,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,1.08907,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,0.402065,1.05896,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.181575,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,2.66432,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.212464,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.135528
}}

Latest revision as of 19:11, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:54691565..54691579,+p2@Higd2a
Mm9::chr4:123395424..123395438,-p1@LOC100504968
p1@Ndufs5
Mm9::chr4:40226422..40226467,-p2@Ndufb6


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:0050136NADH dehydrogenase (quinone) activity0.0294905635102609
GO:0003954NADH dehydrogenase activity0.0294905635102609
GO:0008137NADH dehydrogenase (ubiquinone) activity0.0294905635102609
GO:0016655oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor0.0294905635102609
GO:0016651oxidoreductase activity, acting on NADH or NADPH0.0317627684197563



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
nervous system5.33e-2075
central nervous system6.26e-2073
structure with developmental contribution from neural crest1.28e-1992
regional part of nervous system1.00e-1754
neural tube1.53e-1652
neural rod1.53e-1652
future spinal cord1.53e-1652
neural keel1.53e-1652
gray matter5.40e-1634
brain1.09e-1347
future brain1.09e-1347
regional part of brain1.39e-1346
brain grey matter2.13e-1329
regional part of telencephalon2.13e-1329
telencephalon2.13e-1329
ectoderm-derived structure3.44e-1395
ectoderm3.44e-1395
presumptive ectoderm3.44e-1395
neurectoderm6.64e-1364
neural plate6.64e-1364
presumptive neural plate6.64e-1364
anterior neural tube8.68e-1140
regional part of forebrain2.14e-1039
forebrain2.14e-1039
future forebrain2.14e-1039
cerebral cortex1.02e-0921
cerebral hemisphere1.02e-0921
pallium1.02e-0921
ecto-epithelium1.30e-0973
tube1.67e-09114
anatomical conduit4.48e-09122
regional part of cerebral cortex1.27e-0817
primary circulatory organ1.11e-0718
heart1.11e-0718
primitive heart tube1.11e-0718
primary heart field1.11e-0718
anterior lateral plate mesoderm1.11e-0718
heart tube1.11e-0718
heart primordium1.11e-0718
cardiac mesoderm1.11e-0718
cardiogenic plate1.11e-0718
heart rudiment1.11e-0718
pre-chordal neural plate1.28e-0749
compound organ3.17e-0743
posterior neural tube5.64e-0712
chordal neural plate5.64e-0712


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)
MA0003.10.0699972
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.825079
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.932001
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.557057
MA0056.10
MA0057.10.896032
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.00834468
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.766354
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.11.61065
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.10.151124
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.40695
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.11.39671
MA0160.11.92525
MA0161.10
MA0162.10.166722
MA0163.10.157796
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.288542
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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