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MCL coexpression mm9:2259: Difference between revisions

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{{MCL_coexpression_mm9
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carbohydrate metabolic process;0.000108753326171585;77559,72157,53412!GO:0005975;carbohydrate metabolic process;0.000108753326171585;77559,72157,53412!GO:0005977;glycogen metabolic process;0.000108753326171585;77559,53412!GO:0006073;glucan metabolic process;0.000108753326171585;77559,53412!GO:0006112;energy reserve metabolic process;0.000111309702332188;77559,53412!GO:0005976;polysaccharide metabolic process;0.000144385332420965;77559,53412!GO:0044264;cellular polysaccharide metabolic process;0.000144385332420965;77559,53412!GO:0015980;energy derivation by oxidation of organic compounds;0.00025051326069894;77559,53412!GO:0004133;glycogen debranching enzyme activity;0.000949615588305118;77559!GO:0004614;phosphoglucomutase activity;0.00341805423570848;72157!GO:0008599;protein phosphatase type 1 regulator activity;0.00388393972196418;53412!GO:0016868;intramolecular transferase activity, phosphotransferases;0.00592127149155579;72157!GO:0006091;generation of precursor metabolites and energy;0.00592127149155579;77559,53412!GO:0009250;glucan biosynthetic process;0.00626402959732651;53412!GO:0005978;glycogen biosynthetic process;0.00626402959732651;53412!GO:0033692;cellular polysaccharide biosynthetic process;0.00954259841460151;53412!GO:0000271;polysaccharide biosynthetic process;0.00954259841460151;53412!GO:0016866;intramolecular transferase activity;0.0137483130670221;72157!GO:0019888;protein phosphatase regulator activity;0.0143697388261853;53412!GO:0019208;phosphatase regulator activity;0.0149286012982054;53412!GO:0043284;biopolymer biosynthetic process;0.0263609252893713;53412!GO:0016051;carbohydrate biosynthetic process;0.0305588804811419;53412!GO:0006006;glucose metabolic process;0.0358548525668646;72157!GO:0019318;hexose metabolic process;0.0454764530594491;72157!GO:0005996;monosaccharide metabolic process;0.0454764530594491;72157!GO:0016853;isomerase activity;0.0478532756546137;72157!GO:0043170;macromolecule metabolic 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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!2.57e-12!47;UBERON:0009854!1.13e-08!23;UBERON:0009856!1.13e-08!23;UBERON:0002107!1.34e-08!22;UBERON:0007499!1.34e-08!22;UBERON:0006925!1.34e-08!22;UBERON:0009497!1.34e-08!22;UBERON:0000015!1.34e-08!22;UBERON:0002423!1.34e-08!22;UBERON:0006235!1.34e-08!22;UBERON:0008835!1.34e-08!22;UBERON:0003894!1.34e-08!22;UBERON:0004161!1.34e-08!22;UBERON:0008836!1.34e-08!22;UBERON:0002365!7.28e-08!25;UBERON:0002330!7.28e-08!25;UBERON:0000025!4.98e-07!114
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.128156,0.612053,0.688265,0.483253,0.704257,0.803568,0.96814,0.993085,0.489964,0.755749,0.790506,0.37041,0.81685,1.2551,0,1.02248,0.473993,0.928768,0.683591,0.570433,0.57409,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,1.18815,0.854272,0.503207,0.089443,1.16474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,1.26006,2.88449,1.61988,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.864765,1.50994,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.758875,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,1.70541,1.06633,0.740267,0.580757,2.39857,1.53136,1.25851,0.576517,0.7614,1.51002,0.476467,1.40021,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,1.08088,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,2.27949,1.70745,0.941555,2.27909,0.653418,0.485304,1.4513,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,1.47798
|tfbs_overrepresentation_jaspar=MA0003.1;1.34944,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.981995,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;1.97232,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;0.251896,MA0058.1;1.4226,MA0059.1;0.59559,MA0060.1;1.83511,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.256913,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.0140887,MA0074.1;3.11034,MA0076.1;0.550092,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;1.56748,MA0091.1;0.703314,MA0092.1;1.56822,MA0093.1;1.29026,MA0095.1;0,MA0098.1;0,MA0100.1;1.84237,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;0.869608,MA0114.1;0.43587,MA0115.1;1.25852,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;0.439506,MA0145.1;0.608454,MA0146.1;1.07887,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;1.07321,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;2.52766,MA0065.2;0.212467,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.263609,MA0155.1;1.21457,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;1.1762,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.10667,MA0163.1;0.672192,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;0.440842,MA0102.2;1.8929,MA0258.1;1.89239,MA0259.1;1.12353,MA0442.1;0
}}

Latest revision as of 18:15, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:36811146..36811160,-p1@Ppp1r3c
Mm9::chr3:116510969..116510979,-p10@Agl
Mm9::chr4:99602049..99602137,+p1@Pgm2
Mm9::chr4:99602138..99602149,+p2@Pgm2


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:0044262cellular carbohydrate metabolic process0.000108753326171585
GO:0005975carbohydrate metabolic process0.000108753326171585
GO:0005977glycogen metabolic process0.000108753326171585
GO:0006073glucan metabolic process0.000108753326171585
GO:0006112energy reserve metabolic process0.000111309702332188
GO:0005976polysaccharide metabolic process0.000144385332420965
GO:0044264cellular polysaccharide metabolic process0.000144385332420965
GO:0015980energy derivation by oxidation of organic compounds0.00025051326069894
GO:0004133glycogen debranching enzyme activity0.000949615588305118
GO:0004614phosphoglucomutase activity0.00341805423570848
GO:0008599protein phosphatase type 1 regulator activity0.00388393972196418
GO:0016868intramolecular transferase activity, phosphotransferases0.00592127149155579
GO:0006091generation of precursor metabolites and energy0.00592127149155579
GO:0009250glucan biosynthetic process0.00626402959732651
GO:0005978glycogen biosynthetic process0.00626402959732651
GO:0033692cellular polysaccharide biosynthetic process0.00954259841460151
GO:0000271polysaccharide biosynthetic process0.00954259841460151
GO:0016866intramolecular transferase activity0.0137483130670221
GO:0019888protein phosphatase regulator activity0.0143697388261853
GO:0019208phosphatase regulator activity0.0149286012982054
GO:0043284biopolymer biosynthetic process0.0263609252893713
GO:0016051carbohydrate biosynthetic process0.0305588804811419
GO:0006006glucose metabolic process0.0358548525668646
GO:0019318hexose metabolic process0.0454764530594491
GO:0005996monosaccharide metabolic process0.0454764530594491
GO:0016853isomerase activity0.0478532756546137
GO:0043170macromolecule metabolic process0.0478532756546137



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 tube2.57e-1247
digestive tract diverticulum1.13e-0823
sac1.13e-0823
liver1.34e-0822
epithelial sac1.34e-0822
digestive gland1.34e-0822
epithelium of foregut-midgut junction1.34e-0822
anatomical boundary1.34e-0822
hepatobiliary system1.34e-0822
foregut-midgut junction1.34e-0822
hepatic diverticulum1.34e-0822
liver primordium1.34e-0822
septum transversum1.34e-0822
liver bud1.34e-0822
exocrine gland7.28e-0825
exocrine system7.28e-0825
tube4.98e-07114


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)
MA0003.11.34944
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.981995
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.11.97232
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
MA0057.10.251896
MA0058.11.4226
MA0059.10.59559
MA0060.11.83511
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.0140887
MA0074.13.11034
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.201215
MA0089.10
MA0090.11.56748
MA0091.10.703314
MA0092.11.56822
MA0093.11.29026
MA0095.10
MA0098.10
MA0100.11.84237
MA0101.10.605676
MA0103.10.540576
MA0105.10.313353
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
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
MA0144.10.439506
MA0145.10.608454
MA0146.11.07887
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.21.07321
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.22.52766
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.11.21457
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.11.1762
MA0160.10.71003
MA0161.10
MA0162.10.10667
MA0163.10.672192
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.20.440842
MA0102.21.8929
MA0258.11.89239
MA0259.11.12353
MA0442.10
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