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MCL coexpression mm9:2853: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004119!1.49e-18!118;UBERON:0000925!1.49e-18!118;UBERON:0006595!1.49e-18!118;UBERON:0001007!1.52e-17!116;UBERON:0001555!1.52e-17!116;UBERON:0007026!1.52e-17!116;UBERON:0004921!1.41e-16!114;UBERON:0005409!7.33e-15!47;UBERON:0000160!4.48e-14!31;UBERON:0000344!3.51e-09!15;UBERON:0004923!3.63e-09!24;UBERON:0003929!8.92e-09!55;UBERON:0002365!1.63e-08!25;UBERON:0002330!1.63e-08!25;UBERON:0001242!2.89e-08!13;UBERON:0000060!2.89e-08!13;UBERON:0001262!2.89e-08!13;UBERON:0004786!2.89e-08!13;UBERON:0009854!3.99e-08!23;UBERON:0009856!3.99e-08!23;UBERON:0002107!1.06e-07!22;UBERON:0007499!1.06e-07!22;UBERON:0006925!1.06e-07!22;UBERON:0009497!1.06e-07!22;UBERON:0000015!1.06e-07!22;UBERON:0002423!1.06e-07!22;UBERON:0006235!1.06e-07!22;UBERON:0008835!1.06e-07!22;UBERON:0003894!1.06e-07!22;UBERON:0004161!1.06e-07!22;UBERON:0008836!1.06e-07!22;UBERON:0000490!3.21e-07!66;UBERON:0005256!3.78e-07!45
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.564138,1.71649,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,1.23467,0.870507,0.906098,1.18012,0.933025,0.608226,0,1.14208,0.578045,1.138,0.328717,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.144706,1.38481,0.902078,0.536514,2.16143,0.582863,0.831295,0.261619,0.610669,0.474221,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,1.41919,1.44925,1.882,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,5.69893,0.195254,0.380977,2.41197,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,1.65883,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,1.63106,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,2.53104,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,2.85884,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,1.79877,1.61484,1.32889,1.21423,2.94085,1.11251,0.94678,0.562367,0.904334,2.62466
|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;6.76937,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;0.61552,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;4.47146,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;0.190475,MA0056.1;0,MA0057.1;0.896032,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;0.502699,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;0.121346,MA0074.1;0.911576,MA0076.1;0.657929,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;0.766354,MA0089.1;0,MA0090.1;0.762482,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;2.32176,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;1.46662,MA0117.1;1.34691,MA0119.1;1.70419,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;1.44606,MA0146.1;10.2037,MA0147.1;2.34772,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;1.86813,MA0035.2;0.903829,MA0039.2;1.55941,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;2.10982,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;0.840842,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;8.43962,MA0163.1;0.157796,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;2.17326,MA0099.2;1.06348,MA0079.2;4.46976,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}

Latest revision as of 19:11, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:49063373..49063398,-p2@Fam120a
Mm9::chr13:49063403..49063437,-p1@Fam120a
Mm9::chr6:119338689..119338757,-p2@Adipor2


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:0042562hormone binding0.00657426176518929
GO:0009755hormone-mediated signaling0.00657426176518929
GO:0009725response to hormone stimulus0.0082178272064866
GO:0019395fatty acid oxidation0.0082178272064866
GO:0046982protein heterodimerization activity0.0197227852955679
GO:0006631fatty acid metabolic process0.0388977154440366
GO:0042802identical protein binding0.0388977154440366
GO:0046983protein dimerization activity0.0388977154440366
GO:0032787monocarboxylic acid metabolic process0.0388977154440366
GO:0009719response to endogenous stimulus0.041089136032433



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
endoderm-derived structure1.49e-18118
endoderm1.49e-18118
presumptive endoderm1.49e-18118
digestive system1.52e-17116
digestive tract1.52e-17116
primitive gut1.52e-17116
subdivision of digestive tract1.41e-16114
gastrointestinal system7.33e-1547
intestine4.48e-1431
mucosa3.51e-0915
organ component layer3.63e-0924
gut epithelium8.92e-0955
exocrine gland1.63e-0825
exocrine system1.63e-0825
intestinal mucosa2.89e-0813
anatomical wall2.89e-0813
wall of intestine2.89e-0813
gastrointestinal system mucosa2.89e-0813
digestive tract diverticulum3.99e-0823
sac3.99e-0823
liver1.06e-0722
epithelial sac1.06e-0722
digestive gland1.06e-0722
epithelium of foregut-midgut junction1.06e-0722
anatomical boundary1.06e-0722
hepatobiliary system1.06e-0722
foregut-midgut junction1.06e-0722
hepatic diverticulum1.06e-0722
liver primordium1.06e-0722
septum transversum1.06e-0722
liver bud1.06e-0722
unilaminar epithelium3.21e-0766
trunk mesenchyme3.78e-0745


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
MA0014.16.76937
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
MA0048.14.47146
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
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
MA0073.10.121346
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
MA0106.12.32176
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.11.46662
MA0117.11.34691
MA0119.11.70419
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
MA0145.11.44606
MA0146.110.2037
MA0147.12.34772
MA0148.10.820161
MA0149.10.722227
MA0062.21.86813
MA0035.20.903829
MA0039.21.55941
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.22.10982
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.840842
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.18.43962
MA0163.10.157796
MA0164.10.933981
MA0080.20.64167
MA0018.22.17326
MA0099.21.06348
MA0079.24.46976
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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