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MCL coexpression mm9:3072: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001007!1.75e-19!116;UBERON:0001555!1.75e-19!116;UBERON:0007026!1.75e-19!116;UBERON:0000160!4.62e-19!31;UBERON:0005409!6.62e-19!47;UBERON:0004119!1.15e-18!118;UBERON:0000925!1.15e-18!118;UBERON:0006595!1.15e-18!118;UBERON:0004921!2.12e-18!114;UBERON:0005177!9.03e-17!79;UBERON:0002100!9.12e-13!90;UBERON:0000344!5.46e-12!15;UBERON:0001242!5.41e-11!13;UBERON:0000060!5.41e-11!13;UBERON:0001262!5.41e-11!13;UBERON:0004786!5.41e-11!13;UBERON:0000466!8.55e-11!79;UBERON:0009569!6.71e-10!66;UBERON:0001264!8.68e-09!12;UBERON:0002365!2.36e-08!25;UBERON:0002330!2.36e-08!25;UBERON:0003350!2.93e-08!9;UBERON:0004808!2.93e-08!9;UBERON:0001277!2.93e-08!9;UBERON:0009854!3.79e-08!23;UBERON:0009856!3.79e-08!23;UBERON:0002107!1.98e-07!22;UBERON:0007499!1.98e-07!22;UBERON:0006925!1.98e-07!22;UBERON:0009497!1.98e-07!22;UBERON:0000015!1.98e-07!22;UBERON:0002423!1.98e-07!22;UBERON:0006235!1.98e-07!22;UBERON:0008835!1.98e-07!22;UBERON:0003894!1.98e-07!22;UBERON:0004161!1.98e-07!22;UBERON:0008836!1.98e-07!22
|ontology_enrichment_uberon=UBERON:0001007!1.75e-19!116;UBERON:0001555!1.75e-19!116;UBERON:0007026!1.75e-19!116;UBERON:0000160!4.62e-19!31;UBERON:0005409!6.62e-19!47;UBERON:0004119!1.15e-18!118;UBERON:0000925!1.15e-18!118;UBERON:0006595!1.15e-18!118;UBERON:0004921!2.12e-18!114;UBERON:0005177!9.03e-17!79;UBERON:0002100!9.12e-13!90;UBERON:0000344!5.46e-12!15;UBERON:0001242!5.41e-11!13;UBERON:0000060!5.41e-11!13;UBERON:0001262!5.41e-11!13;UBERON:0004786!5.41e-11!13;UBERON:0000466!8.55e-11!79;UBERON:0009569!6.71e-10!66;UBERON:0001264!8.68e-09!12;UBERON:0002365!2.36e-08!25;UBERON:0002330!2.36e-08!25;UBERON:0003350!2.93e-08!9;UBERON:0004808!2.93e-08!9;UBERON:0001277!2.93e-08!9;UBERON:0009854!3.79e-08!23;UBERON:0009856!3.79e-08!23;UBERON:0002107!1.98e-07!22;UBERON:0007499!1.98e-07!22;UBERON:0006925!1.98e-07!22;UBERON:0009497!1.98e-07!22;UBERON:0000015!1.98e-07!22;UBERON:0002423!1.98e-07!22;UBERON:0006235!1.98e-07!22;UBERON:0008835!1.98e-07!22;UBERON:0003894!1.98e-07!22;UBERON:0004161!1.98e-07!22;UBERON:0008836!1.98e-07!22
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.235304,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.876292,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,1.05917,0.608816,0.144706,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.724277,0.610669,0.922882,0.788421,1.05665,0.859154,0.663409,0.646474,1.12346,0.99279,0.971403,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.181575,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,1.31639,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,1.63106,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,1.1471,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.751419,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.721422,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,1.38188,0.904334,1.34909
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.235304,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.876292,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,1.05917,0.608816,0.144706,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.724277,0.610669,0.922882,0.788421,1.05665,0.859154,0.663409,0.646474,1.12346,0.99279,0.971403,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.181575,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,1.31639,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,1.63106,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,1.1471,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.751419,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.721422,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,1.38188,0.904334,1.34909
|tfbs_overrepresentation_jaspar=MA0003.1;0.245953,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.133574,MA0017.1;1.5346,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;0.353763,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;0.557057,MA0056.1;0,MA0057.1;0.337566,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;1.25521,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;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;0.27999,MA0089.1;0,MA0090.1;0.762482,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;1.51475,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;1.3296,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;1.33779,MA0145.1;0.292366,MA0146.1;0.151124,MA0147.1;1.37022,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;0.0481552,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;1.21648,MA0047.2;0.962424,MA0112.2;0.794478,MA0065.2;0.79573,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;1.54848,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;0.0332569,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}
}}

Revision as of 15:49, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:96583335..96583347,+p3@Igsf5
Mm9::chr5:64203686..64203777,+p1@0610040J01Rik
Mm9::chr7:117792331..117792347,-p@chr7:117792331..117792347
-


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:0030165PDZ domain binding0.0132580945597984
GO:0019904protein domain specific binding0.0216950638251246
GO:0005923tight junction0.0216950638251246
GO:0043296apical junction complex0.0216950638251246
GO:0016327apicolateral plasma membrane0.0216950638251246
GO:0005911intercellular junction0.0301320330904509
GO:0009986cell surface0.0313373144140689
GO:0016337cell-cell adhesion0.0313373144140689



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>

Cell Type
Ontology termp-valuen
epithelial cell7.15e-1025
endodermal cell2.11e-0920
intestinal epithelial cell2.93e-089
epithelial cell of alimentary canal2.93e-089

Uber Anatomy
Ontology termp-valuen
digestive system1.75e-19116
digestive tract1.75e-19116
primitive gut1.75e-19116
intestine4.62e-1931
gastrointestinal system6.62e-1947
endoderm-derived structure1.15e-18118
endoderm1.15e-18118
presumptive endoderm1.15e-18118
subdivision of digestive tract2.12e-18114
trunk region element9.03e-1779
trunk9.12e-1390
mucosa5.46e-1215
intestinal mucosa5.41e-1113
anatomical wall5.41e-1113
wall of intestine5.41e-1113
gastrointestinal system mucosa5.41e-1113
immaterial anatomical entity8.55e-1179
subdivision of trunk6.71e-1066
pancreas8.68e-0912
exocrine gland2.36e-0825
exocrine system2.36e-0825
epithelium of mucosa2.93e-089
gastrointestinal system epithelium2.93e-089
intestinal epithelium2.93e-089
digestive tract diverticulum3.79e-0823
sac3.79e-0823
liver1.98e-0722
epithelial sac1.98e-0722
digestive gland1.98e-0722
epithelium of foregut-midgut junction1.98e-0722
anatomical boundary1.98e-0722
hepatobiliary system1.98e-0722
foregut-midgut junction1.98e-0722
hepatic diverticulum1.98e-0722
liver primordium1.98e-0722
septum transversum1.98e-0722
liver bud1.98e-0722


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)
MA0003.10.245953
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.133574
MA0017.11.5346
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
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.557057
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.11.25521
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
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.11.51475
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
MA0114.11.3296
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
MA0144.11.33779
MA0145.10.292366
MA0146.10.151124
MA0147.11.37022
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.0481552
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.21.21648
MA0047.20.962424
MA0112.20.794478
MA0065.20.79573
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
MA0080.21.54848
MA0018.20.944669
MA0099.21.06348
MA0079.20.0332569
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:3072&oldid=2576467"