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MCL coexpression mm9:3398: Difference between revisions

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{{MCL_coexpression_mm9
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amino acid nitrosylation;0.00169835095600723;69219!GO:0016403;dimethylargininase activity;0.00169835095600723;69219!GO:0016813;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines;0.00577439325042459;69219!GO:0006809;nitric oxide biosynthetic process;0.00577439325042459;69219!GO:0046209;nitric oxide metabolic process;0.00577439325042459;69219!GO:0044271;nitrogen compound biosynthetic process;0.0215124454427583;69219!GO:0016810;hydrolase activity, acting on carbon-nitrogen (but not peptide) 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|gostat_on_MCL_coexpression=GO:0017014;protein amino acid nitrosylation;0.00169835095600723;69219!GO:0016403;dimethylargininase activity;0.00169835095600723;69219!GO:0016813;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines;0.00577439325042459;69219!GO:0006809;nitric oxide biosynthetic process;0.00577439325042459;69219!GO:0046209;nitric oxide metabolic process;0.00577439325042459;69219!GO:0044271;nitrogen compound biosynthetic process;0.0215124454427583;69219!GO:0016810;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds;0.0218359408629501;69219!
|ontology_enrichment_celltype=CL:0000055!3.85e-18!49;CL:0000221!1.27e-16!44;CL:0000133!1.27e-16!44;CL:0002319!1.64e-16!43;CL:0000393!8.89e-13!39;CL:0000211!8.89e-13!39;CL:0002321!3.02e-11!70;CL:0000540!3.07e-11!33;CL:0000047!3.07e-11!33;CL:0000031!3.07e-11!33;CL:0000404!3.07e-11!33;CL:0000117!2.50e-10!23;CL:0000337!2.50e-10!23
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!3.05e-26!75;UBERON:0001017!1.06e-25!73;UBERON:0004121!1.24e-21!95;UBERON:0000924!1.24e-21!95;UBERON:0006601!1.24e-21!95;UBERON:0000073!1.43e-19!54;UBERON:0000025!5.10e-19!114;UBERON:0001049!1.16e-18!52;UBERON:0005068!1.16e-18!52;UBERON:0006241!1.16e-18!52;UBERON:0007135!1.16e-18!52;UBERON:0002346!1.64e-17!64;UBERON:0003075!1.64e-17!64;UBERON:0007284!1.64e-17!64;UBERON:0010371!3.84e-16!73;UBERON:0004111!4.63e-16!122;UBERON:0000955!5.95e-16!47;UBERON:0006238!5.95e-16!47;UBERON:0002020!6.45e-16!34;UBERON:0002616!1.53e-15!46;UBERON:0003080!1.74e-13!40;UBERON:0003528!2.54e-13!29;UBERON:0002791!2.54e-13!29;UBERON:0001893!2.54e-13!29;UBERON:0002780!3.40e-13!39;UBERON:0001890!3.40e-13!39;UBERON:0006240!3.40e-13!39;UBERON:0003056!1.42e-11!49;UBERON:0010314!1.01e-10!92;UBERON:0000956!5.08e-10!21;UBERON:0001869!5.08e-10!21;UBERON:0000203!5.08e-10!21;UBERON:0002107!3.01e-09!22;UBERON:0007499!3.01e-09!22;UBERON:0006925!3.01e-09!22;UBERON:0009497!3.01e-09!22;UBERON:0000015!3.01e-09!22;UBERON:0002423!3.01e-09!22;UBERON:0006235!3.01e-09!22;UBERON:0008835!3.01e-09!22;UBERON:0003894!3.01e-09!22;UBERON:0004161!3.01e-09!22;UBERON:0008836!3.01e-09!22;UBERON:0009854!5.00e-09!23;UBERON:0009856!5.00e-09!23;UBERON:0002365!2.69e-08!25;UBERON:0002330!2.69e-08!25;UBERON:0000922!3.85e-08!320;UBERON:0002619!5.60e-08!17;UBERON:0000468!4.41e-07!333
|tfbs_overrepresentation_for_novel_motifs=2.97491,0.193418,0.722405,0.801166,0.587814,0.81763,2.12177,0.467321,0.479531,2.68971,0.870507,0.906098,1.18012,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,1.55113,1.7585,0.825437,2.79074,0.575271,1.05917,1.47967,0.444545,7.29778,0.902078,0.536514,1.24975,0.582863,0.831295,0.261619,0.610669,0.922882,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,1.6706,0.474956,2.1742,1.44925,1.882,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,2.30787,0.195254,0.99201,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,1.94011,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,3.34241,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,1.32874,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,1.34909
|tfbs_overrepresentation_jaspar=MA0003.1;3.77865,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.416365,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;1.49373,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;0.932001,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;0.190475,MA0056.1;0,MA0057.1;0.337566,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;2.1699,MA0061.1;0.5406,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;0.343188,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;0.00834468,MA0074.1;0.911576,MA0076.1;1.58243,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.27999,MA0089.1;0,MA0090.1;1.7994,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;0.62555,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;0.71579,MA0103.1;0.647985,MA0105.1;0.405648,MA0106.1;1.01755,MA0107.1;0.640607,MA0108.2;1.10817,MA0109.1;0,MA0111.1;0.778753,MA0113.1;0.986839,MA0114.1;0.537669,MA0115.1;1.38041,MA0116.1;0.602598,MA0117.1;1.34691,MA0119.1;0.716476,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;0.933582,MA0139.1;0.462282,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;0.541532,MA0145.1;0.794492,MA0146.1;1.44443,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;0.40695,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;0.48458,MA0047.2;0.962424,MA0112.2;0.29236,MA0065.2;0.292912,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;0.35067,MA0155.1;0.312898,MA0156.1;1.58027,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;0.166722,MA0163.1;0.157796,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;0.00937321,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}

Latest revision as of 20:02, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr3:145421682..145421702,+p1@Ddah1
Mm9::chr3:145421714..145421728,+p2@Ddah1
Mm9::chr8:128946461..128946475,+p3@1810063B05Rik


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:0017014protein amino acid nitrosylation0.00169835095600723
GO:0016403dimethylargininase activity0.00169835095600723
GO:0016813hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines0.00577439325042459
GO:0006809nitric oxide biosynthetic process0.00577439325042459
GO:0046209nitric oxide metabolic process0.00577439325042459
GO:0044271nitrogen compound biosynthetic process0.0215124454427583
GO:0016810hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.0218359408629501



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 system3.05e-2675
central nervous system1.06e-2573
ectoderm-derived structure1.24e-2195
ectoderm1.24e-2195
presumptive ectoderm1.24e-2195
regional part of nervous system1.43e-1954
tube5.10e-19114
neural tube1.16e-1852
neural rod1.16e-1852
future spinal cord1.16e-1852
neural keel1.16e-1852
neurectoderm1.64e-1764
neural plate1.64e-1764
presumptive neural plate1.64e-1764
ecto-epithelium3.84e-1673
anatomical conduit4.63e-16122
brain5.95e-1647
future brain5.95e-1647
gray matter6.45e-1634
regional part of brain1.53e-1546
anterior neural tube1.74e-1340
brain grey matter2.54e-1329
regional part of telencephalon2.54e-1329
telencephalon2.54e-1329
regional part of forebrain3.40e-1339
forebrain3.40e-1339
future forebrain3.40e-1339
pre-chordal neural plate1.42e-1149
structure with developmental contribution from neural crest1.01e-1092
cerebral cortex5.08e-1021
cerebral hemisphere5.08e-1021
pallium5.08e-1021
liver3.01e-0922
epithelial sac3.01e-0922
digestive gland3.01e-0922
epithelium of foregut-midgut junction3.01e-0922
anatomical boundary3.01e-0922
hepatobiliary system3.01e-0922
foregut-midgut junction3.01e-0922
hepatic diverticulum3.01e-0922
liver primordium3.01e-0922
septum transversum3.01e-0922
liver bud3.01e-0922
digestive tract diverticulum5.00e-0923
sac5.00e-0923
exocrine gland2.69e-0825
exocrine system2.69e-0825
embryo3.85e-08320
regional part of cerebral cortex5.60e-0817
multi-cellular organism4.41e-07333


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)
MA0003.13.77865
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.416365
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.11.49373
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
MA0055.10.190475
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.12.1699
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
MA0076.11.58243
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.11.7994
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
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.794492
MA0146.11.44443
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
MA0156.11.58027
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.157796
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.00937321
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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