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MCL coexpression mm9:1328: Difference between revisions

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{{MCL_coexpression_mm9
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metabolic process;0.00056300435164188;244416,110095!GO:0005977;glycogen metabolic process;0.00056300435164188;244416,110095!GO:0006112;energy reserve metabolic process;0.00056300435164188;244416,110095!GO:0005976;polysaccharide metabolic process;0.000613183580318231;244416,110095!GO:0044264;cellular polysaccharide metabolic process;0.000613183580318231;244416,110095!GO:0015980;energy derivation by oxidation of organic compounds;0.00101252787028551;244416,110095!GO:0008184;glycogen phosphorylase activity;0.0049459428233834;110095!GO:0004645;phosphorylase activity;0.00865397733034007;110095!GO:0044262;cellular carbohydrate metabolic process;0.00951050988939786;244416,110095!GO:0005975;carbohydrate metabolic process;0.0166545253887196;244416,110095!GO:0006091;generation of precursor metabolites and energy;0.0209472227611453;244416,110095!GO:0006749;glutathione metabolic process;0.0259106685090976;56615!GO:0000267;cell fraction;0.0259106685090976;56615,110095!GO:0004364;glutathione transferase 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|gostat_on_MCL_coexpression=GO:0006073;glucan metabolic process;0.00056300435164188;244416,110095!GO:0005977;glycogen metabolic process;0.00056300435164188;244416,110095!GO:0006112;energy reserve metabolic process;0.00056300435164188;244416,110095!GO:0005976;polysaccharide metabolic process;0.000613183580318231;244416,110095!GO:0044264;cellular polysaccharide metabolic process;0.000613183580318231;244416,110095!GO:0015980;energy derivation by oxidation of organic compounds;0.00101252787028551;244416,110095!GO:0008184;glycogen phosphorylase activity;0.0049459428233834;110095!GO:0004645;phosphorylase activity;0.00865397733034007;110095!GO:0044262;cellular carbohydrate metabolic process;0.00951050988939786;244416,110095!GO:0005975;carbohydrate metabolic process;0.0166545253887196;244416,110095!GO:0006091;generation of precursor metabolites and energy;0.0209472227611453;244416,110095!GO:0006749;glutathione metabolic process;0.0259106685090976;56615!GO:0000267;cell fraction;0.0259106685090976;56615,110095!GO:0004364;glutathione transferase activity;0.0283901252252494;56615!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!2.34e-09!47;UBERON:0002107!6.45e-08!22;UBERON:0007499!6.45e-08!22;UBERON:0006925!6.45e-08!22;UBERON:0009497!6.45e-08!22;UBERON:0000015!6.45e-08!22;UBERON:0002423!6.45e-08!22;UBERON:0006235!6.45e-08!22;UBERON:0008835!6.45e-08!22;UBERON:0003894!6.45e-08!22;UBERON:0004161!6.45e-08!22;UBERON:0008836!6.45e-08!22;UBERON:0009569!9.11e-08!66;UBERON:0002365!1.74e-07!25;UBERON:0002330!1.74e-07!25;UBERON:0009854!1.81e-07!23;UBERON:0009856!1.81e-07!23;UBERON:0005256!4.14e-07!45
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.0600685,0.464605,0.535892,0.346849,0.550971,0.645383,0.691572,0.257202,1.48899,0.599767,1.53013,0.247704,0.6581,0.955327,0,0.856992,0.89822,0.656199,0.86893,0.426133,0.713088,0.657163,0.345236,0.472505,0.686615,0.63639,0.572827,0.394364,0.534301,0.558142,0.960397,0.336199,0.589948,0.364821,0.607065,0.871288,0.629145,0.303703,0.27383,0.342638,1.38433,0.327433,0.366415,0.161543,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.269393,0.827522,1.62226,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.366795,1.156,0.599223,1.70884,0.204132,0.763395,0.922432,1.10012,0.254777,0.874787,0.722675,0.240896,1.03903,0.0539203,0.220054,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,1.10269,0.605144,1.33732,0.340765,0.247162,0.53982,0.858327,0.862623,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,1.67297,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,1.03315,0.325363,1.10596,0.287383,0.678689,1.18867,1.70209,0.983048,0.48935,2.16235,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,0.0323861
|tfbs_overrepresentation_jaspar=MA0003.1;0.476238,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.558098,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.969171,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.486223,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.0585191,MA0056.1;0,MA0057.1;0.149949,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;0.275911,MA0061.1;1.49922,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.911705,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.0477423,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.358337,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;0.379257,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;0.398766,MA0105.1;1.72386,MA0106.1;0.737893,MA0107.1;0.392331,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.944657,MA0117.1;1.05576,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;1.2655,MA0140.1;0.625902,MA0141.1;1.07584,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;0.379391,MA0146.1;0.635245,MA0147.1;0.858298,MA0148.1;0.553294,MA0149.1;3.03063,MA0062.2;1.11803,MA0035.2;0.630778,MA0039.2;0.328366,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;0.723439,MA0047.2;0.685741,MA0112.2;0.119197,MA0065.2;0.119561,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;1.49271,MA0155.1;0.414701,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;1.08528,MA0163.1;1.03138,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.147137,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
}}

Latest revision as of 16:45, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:71328609..71328626,-p1@Pygl
Mm9::chr1:183187792..183187805,-p@chr1:183187792..183187805
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Mm9::chr6:138088819..138088841,+p2@Mgst1
Mm9::chr8:36439699..36439722,+p1@Ppp1r3b
Mm9::chr8:36439734..36439750,+p3@Ppp1r3b
Mm9::chrX:138662827..138662849,+p3@Nxt2


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:0006073glucan metabolic process0.00056300435164188
GO:0005977glycogen metabolic process0.00056300435164188
GO:0006112energy reserve metabolic process0.00056300435164188
GO:0005976polysaccharide metabolic process0.000613183580318231
GO:0044264cellular polysaccharide metabolic process0.000613183580318231
GO:0015980energy derivation by oxidation of organic compounds0.00101252787028551
GO:0008184glycogen phosphorylase activity0.0049459428233834
GO:0004645phosphorylase activity0.00865397733034007
GO:0044262cellular carbohydrate metabolic process0.00951050988939786
GO:0005975carbohydrate metabolic process0.0166545253887196
GO:0006091generation of precursor metabolites and energy0.0209472227611453
GO:0006749glutathione metabolic process0.0259106685090976
GO:0000267cell fraction0.0259106685090976
GO:0004364glutathione transferase activity0.0283901252252494



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
epithelial tube2.34e-0947
liver6.45e-0822
epithelial sac6.45e-0822
digestive gland6.45e-0822
epithelium of foregut-midgut junction6.45e-0822
anatomical boundary6.45e-0822
hepatobiliary system6.45e-0822
foregut-midgut junction6.45e-0822
hepatic diverticulum6.45e-0822
liver primordium6.45e-0822
septum transversum6.45e-0822
liver bud6.45e-0822
subdivision of trunk9.11e-0866
exocrine gland1.74e-0725
exocrine system1.74e-0725
digestive tract diverticulum1.81e-0723
sac1.81e-0723
trunk mesenchyme4.14e-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)
MA0003.10.476238
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.10.558098
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.969171
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.486223
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.149949
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.11.49922
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.911705
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.0477423
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.11.72386
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.944657
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.11.2655
MA0140.10.625902
MA0141.11.07584
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.379391
MA0146.10.635245
MA0147.10.858298
MA0148.10.553294
MA0149.13.03063
MA0062.21.11803
MA0035.20.630778
MA0039.20.328366
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.723439
MA0047.20.685741
MA0112.20.119197
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.11.49271
MA0155.10.414701
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.11.08528
MA0163.11.03138
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.147137
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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