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MCL coexpression mm9:2145: Difference between revisions

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{{MCL_coexpression_mm9
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1-dehydrogenase activity;0.00777911685918377;100198!GO:0017057;6-phosphogluconolactonase activity;0.00777911685918377;100198!GO:0004345;glucose-6-phosphate dehydrogenase activity;0.00777911685918377;100198!GO:0006098;pentose-phosphate shunt;0.0124448820561999;100198!GO:0006740;NADPH regeneration;0.0124448820561999;100198!GO:0006739;NADP metabolic process;0.0181458027245934;100198!GO:0006769;nicotinamide metabolic process;0.0226121789953236;100198!GO:0019362;pyridine nucleotide metabolic process;0.0226121789953236;100198!GO:0005925;focal adhesion;0.0226121789953236;225341!GO:0005924;cell-substrate adherens junction;0.0226121789953236;225341!GO:0006733;oxidoreduction coenzyme metabolic process;0.0226121789953236;100198!GO:0030055;cell-matrix junction;0.0226692001235209;225341!GO:0006767;water-soluble vitamin metabolic process;0.0233143341778803;100198!GO:0006007;glucose catabolic process;0.025343456383576;100198!GO:0046365;monosaccharide catabolic process;0.025343456383576;100198!GO:0019320;hexose catabolic process;0.025343456383576;100198!GO:0046164;alcohol catabolic process;0.025343456383576;100198!GO:0005912;adherens junction;0.025343456383576;225341!GO:0006766;vitamin metabolic process;0.025343456383576;100198!GO:0044275;cellular carbohydrate catabolic process;0.0254108027034711;100198!GO:0016323;basolateral plasma membrane;0.0254108027034711;225341!GO:0016052;carbohydrate catabolic process;0.0254108027034711;100198!GO:0006006;glucose metabolic process;0.032723093673353;100198!GO:0004091;carboxylesterase activity;0.0336162331405122;100198!GO:0016616;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;0.0341277797270279;100198!GO:0016614;oxidoreductase activity, acting on CH-OH group of donors;0.0354912718992774;100198!GO:0019318;hexose metabolic process;0.0370950229187441;100198!GO:0005996;monosaccharide metabolic 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|gostat_on_MCL_coexpression=GO:0047936;glucose 1-dehydrogenase activity;0.00777911685918377;100198!GO:0017057;6-phosphogluconolactonase activity;0.00777911685918377;100198!GO:0004345;glucose-6-phosphate dehydrogenase activity;0.00777911685918377;100198!GO:0006098;pentose-phosphate shunt;0.0124448820561999;100198!GO:0006740;NADPH regeneration;0.0124448820561999;100198!GO:0006739;NADP metabolic process;0.0181458027245934;100198!GO:0006769;nicotinamide metabolic process;0.0226121789953236;100198!GO:0019362;pyridine nucleotide metabolic process;0.0226121789953236;100198!GO:0005925;focal adhesion;0.0226121789953236;225341!GO:0005924;cell-substrate adherens junction;0.0226121789953236;225341!GO:0006733;oxidoreduction coenzyme metabolic process;0.0226121789953236;100198!GO:0030055;cell-matrix junction;0.0226692001235209;225341!GO:0006767;water-soluble vitamin metabolic process;0.0233143341778803;100198!GO:0006007;glucose catabolic process;0.025343456383576;100198!GO:0046365;monosaccharide catabolic process;0.025343456383576;100198!GO:0019320;hexose catabolic process;0.025343456383576;100198!GO:0046164;alcohol catabolic process;0.025343456383576;100198!GO:0005912;adherens junction;0.025343456383576;225341!GO:0006766;vitamin metabolic process;0.025343456383576;100198!GO:0044275;cellular carbohydrate catabolic process;0.0254108027034711;100198!GO:0016323;basolateral plasma membrane;0.0254108027034711;225341!GO:0016052;carbohydrate catabolic process;0.0254108027034711;100198!GO:0006006;glucose metabolic process;0.032723093673353;100198!GO:0004091;carboxylesterase activity;0.0336162331405122;100198!GO:0016616;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;0.0341277797270279;100198!GO:0016614;oxidoreductase activity, acting on CH-OH group of donors;0.0354912718992774;100198!GO:0019318;hexose metabolic process;0.0370950229187441;100198!GO:0005996;monosaccharide metabolic process;0.0370950229187441;100198!GO:0005792;microsome;0.0397288219619067;100198!GO:0042598;vesicular fraction;0.0397288219619067;100198!GO:0006732;coenzyme metabolic process;0.0397288219619067;100198!GO:0009117;nucleotide metabolic process;0.0437860630783343;100198!GO:0051186;cofactor metabolic process;0.0438594544916371;100198!GO:0055086;nucleobase, nucleoside and nucleotide metabolic process;0.0441544680719521;100198!GO:0044265;cellular macromolecule catabolic process;0.0497044630990999;100198!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002100!1.17e-16!90;UBERON:0005177!1.79e-15!79;UBERON:0009569!3.39e-15!66;UBERON:0005256!1.30e-12!45;UBERON:0005172!1.77e-12!49;UBERON:0005173!1.77e-12!49;UBERON:0002417!1.77e-12!49;UBERON:0000916!1.77e-12!49;UBERON:0003104!1.17e-11!61;UBERON:0009142!1.17e-11!61;UBERON:0002365!3.17e-10!25;UBERON:0002330!3.17e-10!25;UBERON:0000466!3.34e-10!79;UBERON:0002107!1.84e-09!22;UBERON:0007499!1.84e-09!22;UBERON:0006925!1.84e-09!22;UBERON:0009497!1.84e-09!22;UBERON:0000015!1.84e-09!22;UBERON:0002423!1.84e-09!22;UBERON:0006235!1.84e-09!22;UBERON:0008835!1.84e-09!22;UBERON:0003894!1.84e-09!22;UBERON:0004161!1.84e-09!22;UBERON:0008836!1.84e-09!22;UBERON:0009854!3.48e-09!23;UBERON:0009856!3.48e-09!23;UBERON:0003914!2.00e-08!47
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.402508,0.612053,0.688265,0.483253,0.704257,0.803568,0.96814,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.683591,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,1.62441,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.318879,0.503207,0.623685,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.544696,0.504971,0.0986756,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.323563,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.731844,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.143825,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.0824127
|tfbs_overrepresentation_jaspar=MA0003.1;0.142214,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.0809287,MA0017.1;1.30949,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;3.08637,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;1.16866,MA0041.1;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;0.735223,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;0.125758,MA0056.1;0,MA0057.1;0.701847,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;0.403071,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.713436,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.0471131,MA0074.1;0.795862,MA0076.1;1.35592,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.201215,MA0089.1;0,MA0090.1;0.650768,MA0091.1;1.67688,MA0092.1;0.651119,MA0093.1;0.519148,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;0.540576,MA0105.1;0.313353,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;3.3407,MA0114.1;1.11164,MA0115.1;2.80994,MA0116.1;0.497293,MA0117.1;1.22527,MA0119.1;0.606338,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.365453,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;1.11951,MA0145.1;0.21199,MA0146.1;0.0944145,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;0.238019,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;0.211985,MA0065.2;1.14711,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.263609,MA0155.1;0.230016,MA0156.1;1.35382,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.346529,MA0163.1;0.0996272,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;0.0234849,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}

Latest revision as of 18:04, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:66978015..66978059,-p@chr15:66978015..66978059
-
Mm9::chr18:32091124..32091174,+p1@Lims2
Mm9::chr4:149377244..149377258,-p3@H6pd
Mm9::chr4:149377276..149377303,-p2@H6pd


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:0047936glucose 1-dehydrogenase activity0.00777911685918377
GO:00170576-phosphogluconolactonase activity0.00777911685918377
GO:0004345glucose-6-phosphate dehydrogenase activity0.00777911685918377
GO:0006098pentose-phosphate shunt0.0124448820561999
GO:0006740NADPH regeneration0.0124448820561999
GO:0006739NADP metabolic process0.0181458027245934
GO:0006769nicotinamide metabolic process0.0226121789953236
GO:0019362pyridine nucleotide metabolic process0.0226121789953236
GO:0005925focal adhesion0.0226121789953236
GO:0005924cell-substrate adherens junction0.0226121789953236
GO:0006733oxidoreduction coenzyme metabolic process0.0226121789953236
GO:0030055cell-matrix junction0.0226692001235209
GO:0006767water-soluble vitamin metabolic process0.0233143341778803
GO:0006007glucose catabolic process0.025343456383576
GO:0046365monosaccharide catabolic process0.025343456383576
GO:0019320hexose catabolic process0.025343456383576
GO:0046164alcohol catabolic process0.025343456383576
GO:0005912adherens junction0.025343456383576
GO:0006766vitamin metabolic process0.025343456383576
GO:0044275cellular carbohydrate catabolic process0.0254108027034711
GO:0016323basolateral plasma membrane0.0254108027034711
GO:0016052carbohydrate catabolic process0.0254108027034711
GO:0006006glucose metabolic process0.032723093673353
GO:0004091carboxylesterase activity0.0336162331405122
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.0341277797270279
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0354912718992774
GO:0019318hexose metabolic process0.0370950229187441
GO:0005996monosaccharide metabolic process0.0370950229187441
GO:0005792microsome0.0397288219619067
GO:0042598vesicular fraction0.0397288219619067
GO:0006732coenzyme metabolic process0.0397288219619067
GO:0009117nucleotide metabolic process0.0437860630783343
GO:0051186cofactor metabolic process0.0438594544916371
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0441544680719521
GO:0044265cellular macromolecule catabolic process0.0497044630990999



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>


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)
MA0003.10.142214
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.0809287
MA0017.11.30949
MA0019.10.964875
MA0024.11.11019
MA0025.13.08637
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.10.735223
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.125758
MA0056.10
MA0057.10.701847
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.713436
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.0471131
MA0074.10.795862
MA0076.11.35592
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.201215
MA0089.10
MA0090.10.650768
MA0091.11.67688
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.313353
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.13.3407
MA0114.11.11164
MA0115.12.80994
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.365453
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.11.11951
MA0145.10.21199
MA0146.10.0944145
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.20.238019
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.20.211985
MA0065.21.14711
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.230016
MA0156.11.35382
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.346529
MA0163.10.0996272
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.20.0234849
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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