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MCL coexpression mm9:2868: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0005256!4.20e-11!45;UBERON:0003104!1.40e-10!61;UBERON:0009142!1.40e-10!61;UBERON:0004119!1.73e-10!118;UBERON:0000925!1.73e-10!118;UBERON:0006595!1.73e-10!118;UBERON:0001007!2.17e-10!116;UBERON:0001555!2.17e-10!116;UBERON:0007026!2.17e-10!116;UBERON:0004921!1.14e-09!114;UBERON:0002365!5.45e-09!25;UBERON:0002330!5.45e-09!25;UBERON:0009854!6.84e-09!23;UBERON:0009856!6.84e-09!23;UBERON:0000160!1.54e-08!31;UBERON:0002107!1.68e-08!22;UBERON:0007499!1.68e-08!22;UBERON:0006925!1.68e-08!22;UBERON:0009497!1.68e-08!22;UBERON:0000015!1.68e-08!22;UBERON:0002423!1.68e-08!22;UBERON:0006235!1.68e-08!22;UBERON:0008835!1.68e-08!22;UBERON:0003894!1.68e-08!22;UBERON:0004161!1.68e-08!22;UBERON:0008836!1.68e-08!22;UBERON:0005409!2.47e-08!47;UBERON:0002100!3.57e-08!90;UBERON:0003914!3.75e-08!47;UBERON:0009569!2.34e-07!66;UBERON:0005172!2.48e-07!49;UBERON:0005173!2.48e-07!49;UBERON:0002417!2.48e-07!49;UBERON:0000916!2.48e-07!49
|ontology_enrichment_uberon=UBERON:0005256!4.20e-11!45;UBERON:0003104!1.40e-10!61;UBERON:0009142!1.40e-10!61;UBERON:0004119!1.73e-10!118;UBERON:0000925!1.73e-10!118;UBERON:0006595!1.73e-10!118;UBERON:0001007!2.17e-10!116;UBERON:0001555!2.17e-10!116;UBERON:0007026!2.17e-10!116;UBERON:0004921!1.14e-09!114;UBERON:0002365!5.45e-09!25;UBERON:0002330!5.45e-09!25;UBERON:0009854!6.84e-09!23;UBERON:0009856!6.84e-09!23;UBERON:0000160!1.54e-08!31;UBERON:0002107!1.68e-08!22;UBERON:0007499!1.68e-08!22;UBERON:0006925!1.68e-08!22;UBERON:0009497!1.68e-08!22;UBERON:0000015!1.68e-08!22;UBERON:0002423!1.68e-08!22;UBERON:0006235!1.68e-08!22;UBERON:0008835!1.68e-08!22;UBERON:0003894!1.68e-08!22;UBERON:0004161!1.68e-08!22;UBERON:0008836!1.68e-08!22;UBERON:0005409!2.47e-08!47;UBERON:0002100!3.57e-08!90;UBERON:0003914!3.75e-08!47;UBERON:0009569!2.34e-07!66;UBERON:0005172!2.48e-07!49;UBERON:0005173!2.48e-07!49;UBERON:0002417!2.48e-07!49;UBERON:0000916!2.48e-07!49
|tfbs_overrepresentation_for_novel_motifs=0.752782,1.07244,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.144706,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.156582,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,1.07031,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.535545,0.568545,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.609576,0.805461,1.14346,1.37508,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,1.37701,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.999018,0.721422,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,1.95046
|tfbs_overrepresentation_for_novel_motifs=0.752782,1.07244,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.144706,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.156582,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,1.07031,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.535545,0.568545,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.609576,0.805461,1.14346,1.37508,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,1.37701,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.999018,0.721422,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,1.95046
|tfbs_overrepresentation_jaspar=MA0003.1;1.35193,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.825079,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;1.69964,MA0042.1;1.66761,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;0.353763,MA0050.1;1.97065,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;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;1.69369,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;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;1.3296,MA0115.1;1.38041,MA0116.1;0.602598,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;0.292366,MA0146.1;0.900029,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;0.71803,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;1.44804,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;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;0.499274,MA0163.1;0.157796,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;0.288542,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}
}}

Revision as of 15:30, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:64230613..64230656,-p1@Slc35d2
Mm9::chr14:65059705..65059760,-p1@Msra
Mm9::chr18:24812357..24812384,+p1@Mocos


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:0008113peptide-methionine-(S)-S-oxide reductase activity0.0088249089173742
GO:0006777Mo-molybdopterin cofactor biosynthetic process0.0088249089173742
GO:0043545molybdopterin cofactor metabolic process0.0088249089173742
GO:0019720Mo-molybdopterin cofactor metabolic process0.0088249089173742
GO:0032324molybdopterin cofactor biosynthetic process0.0088249089173742
GO:0030151molybdenum ion binding0.0088249089173742
GO:0016671oxidoreductase activity, acting on sulfur group of donors, disulfide as acceptor0.0088249089173742
GO:0042559pteridine and derivative biosynthetic process0.010035583815854
GO:0019438aromatic compound biosynthetic process0.010035583815854
GO:0042558pteridine and derivative metabolic process0.010035583815854
GO:0016667oxidoreductase activity, acting on sulfur group of donors0.0140303979737369
GO:0008483transaminase activity0.017355957008127
GO:0016769transferase activity, transferring nitrogenous groups0.0187899215836456
GO:0005351sugar:hydrogen ion symporter activity0.0187899215836456
GO:0051119sugar transmembrane transporter activity0.0187899215836456
GO:0015144carbohydrate transmembrane transporter activity0.0187899215836456
GO:0030170pyridoxal phosphate binding0.0208507923801405
GO:0008643carbohydrate transport0.0265186708507003
GO:0009108coenzyme biosynthetic process0.0335936131658487
GO:0051188cofactor biosynthetic process0.0368861757135079
GO:0019842vitamin binding0.0384041233135154
GO:0006725aromatic compound metabolic process0.0394341859602444
GO:0015293symporter activity0.0443469714640387
GO:0016829lyase activity0.0485198264210325
GO:0006732coenzyme metabolic process0.0487053843079881
GO:0048037cofactor binding0.0494585072045406
GO:0015291secondary active transmembrane transporter activity0.0498727161413483



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
trunk mesenchyme4.20e-1145
mesenchyme1.40e-1061
entire embryonic mesenchyme1.40e-1061
endoderm-derived structure1.73e-10118
endoderm1.73e-10118
presumptive endoderm1.73e-10118
digestive system2.17e-10116
digestive tract2.17e-10116
primitive gut2.17e-10116
subdivision of digestive tract1.14e-09114
exocrine gland5.45e-0925
exocrine system5.45e-0925
digestive tract diverticulum6.84e-0923
sac6.84e-0923
intestine1.54e-0831
liver1.68e-0822
epithelial sac1.68e-0822
digestive gland1.68e-0822
epithelium of foregut-midgut junction1.68e-0822
anatomical boundary1.68e-0822
hepatobiliary system1.68e-0822
foregut-midgut junction1.68e-0822
hepatic diverticulum1.68e-0822
liver primordium1.68e-0822
septum transversum1.68e-0822
liver bud1.68e-0822
gastrointestinal system2.47e-0847
trunk3.57e-0890
epithelial tube3.75e-0847
subdivision of trunk2.34e-0766
abdomen element2.48e-0749
abdominal segment element2.48e-0749
abdominal segment of trunk2.48e-0749
abdomen2.48e-0749


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)
MA0003.11.35193
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.825079
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
MA0041.11.69964
MA0042.11.66761
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.11.97065
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.337566
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
MA0073.11.69369
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
MA0093.10.62555
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
MA0114.11.3296
MA0115.11.38041
MA0116.10.602598
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
MA0145.10.292366
MA0146.10.900029
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.71803
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.21.44804
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
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.499274
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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