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MCL coexpression mm9:1976: Difference between revisions

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{{MCL_coexpression_mm9
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metabolic process;0.000306281834683947;18563,20787,235623!GO:0044255;cellular lipid metabolic process;0.00102675017073312;18563,20787,235623!GO:0006629;lipid metabolic process;0.00102675017073312;18563,20787,235623!GO:0008203;cholesterol metabolic process;0.00102675017073312;20787,235623!GO:0016125;sterol metabolic process;0.00102675017073312;20787,235623!GO:0004736;pyruvate carboxylase activity;0.00250629676560923;18563!GO:0032810;sterol response element binding;0.00250629676560923;20787!GO:0008202;steroid metabolic process;0.00250629676560923;20787,235623!GO:0032787;monocarboxylic acid metabolic process;0.00515569378181183;18563,235623!GO:0009374;biotin binding;0.00755915840589375;18563!GO:0009267;cellular response to starvation;0.00944739489749404;20787!GO:0019217;regulation of fatty acid metabolic process;0.00944739489749404;235623!GO:0016885;ligase activity, forming carbon-carbon bonds;0.00944739489749404;18563!GO:0031669;cellular response to nutrient 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|gostat_on_MCL_coexpression=GO:0006066;alcohol metabolic process;0.000306281834683947;18563,20787,235623!GO:0044255;cellular lipid metabolic process;0.00102675017073312;18563,20787,235623!GO:0006629;lipid metabolic process;0.00102675017073312;18563,20787,235623!GO:0008203;cholesterol metabolic process;0.00102675017073312;20787,235623!GO:0016125;sterol metabolic process;0.00102675017073312;20787,235623!GO:0004736;pyruvate carboxylase activity;0.00250629676560923;18563!GO:0032810;sterol response element binding;0.00250629676560923;20787!GO:0008202;steroid metabolic process;0.00250629676560923;20787,235623!GO:0032787;monocarboxylic acid metabolic process;0.00515569378181183;18563,235623!GO:0009374;biotin binding;0.00755915840589375;18563!GO:0009267;cellular response to starvation;0.00944739489749404;20787!GO:0019217;regulation of fatty acid metabolic process;0.00944739489749404;235623!GO:0016885;ligase activity, forming carbon-carbon bonds;0.00944739489749404;18563!GO:0031669;cellular response to nutrient levels;0.00944739489749404;20787!GO:0015485;cholesterol binding;0.0100020277963888;235623!GO:0042594;response to starvation;0.0100020277963888;20787!GO:0031668;cellular response to extracellular stimulus;0.0100020277963888;20787!GO:0019752;carboxylic acid metabolic process;0.0107367492345269;18563,235623!GO:0006082;organic acid metabolic process;0.0107367492345269;18563,235623!GO:0031667;response to nutrient levels;0.0122775759449278;20787!GO:0032934;sterol binding;0.0123172879608904;235623!GO:0031090;organelle membrane;0.0123172879608904;18563,235623!GO:0009991;response to extracellular stimulus;0.0123172879608904;20787!GO:0033554;cellular response to stress;0.0128414179677663;20787!GO:0006094;gluconeogenesis;0.0128414179677663;18563!GO:0019216;regulation of lipid metabolic process;0.0137986537725932;235623!GO:0051716;cellular response to stimulus;0.0139861729210222;20787!GO:0006090;pyruvate metabolic process;0.0141602239531468;18563!GO:0019319;hexose biosynthetic process;0.0147469997075971;18563!GO:0005783;endoplasmic reticulum;0.0147469997075971;20787,235623!GO:0046165;alcohol biosynthetic process;0.0147469997075971;18563!GO:0046364;monosaccharide biosynthetic process;0.0147469997075971;18563!GO:0044444;cytoplasmic part;0.0163733969640664;18563,20787,235623!GO:0005496;steroid binding;0.0260620613217157;235623!GO:0005789;endoplasmic reticulum membrane;0.0376592756433307;235623!GO:0042175;nuclear envelope-endoplasmic reticulum network;0.0381760376023527;235623!GO:0016051;carbohydrate biosynthetic process;0.0396196000953267;18563!GO:0044432;endoplasmic reticulum part;0.0396196000953267;235623!GO:0006006;glucose metabolic process;0.0467633555420892;18563!GO:0019842;vitamin binding;0.0493329562777339;18563!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002365!8.32e-12!25;UBERON:0002330!8.32e-12!25;UBERON:0009854!9.38e-11!23;UBERON:0009856!9.38e-11!23;UBERON:0002107!2.36e-10!22;UBERON:0007499!2.36e-10!22;UBERON:0006925!2.36e-10!22;UBERON:0009497!2.36e-10!22;UBERON:0000015!2.36e-10!22;UBERON:0002423!2.36e-10!22;UBERON:0006235!2.36e-10!22;UBERON:0008835!2.36e-10!22;UBERON:0003894!2.36e-10!22;UBERON:0004161!2.36e-10!22;UBERON:0008836!2.36e-10!22;UBERON:0005172!5.05e-09!49;UBERON:0005173!5.05e-09!49;UBERON:0002417!5.05e-09!49;UBERON:0000916!5.05e-09!49;UBERON:0005256!1.75e-08!45;UBERON:0005177!9.16e-07!79
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.128156,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.993085,2.16739,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.683591,0.570433,0.57409,0.815872,0.481455,0.620553,0.846564,0.906602,0.727368,0.535752,0.290745,0.711848,1.12823,1.18815,0.318879,0.503207,0.089443,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.0986756,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,2.87856,0.82458,0.549352,0.776619,0.882473,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,1.12016,1.32691,0.323563,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,2.70843,0.758875,0.129654,0.791209,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,1.09896,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,1.4032,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,1.40021,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.79777,0.184289,1.27621,1.069,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.0824127
}}

Latest revision as of 17:48, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:60023912..60023930,-p1@Srebf1
Mm9::chr19:4510510..4510532,+p1@Pcx
Mm9::chr19:4510536..4510552,+p2@Pcx
Mm9::chr9:110235906..110235939,+p1@Scap


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:0006066alcohol metabolic process0.000306281834683947
GO:0044255cellular lipid metabolic process0.00102675017073312
GO:0006629lipid metabolic process0.00102675017073312
GO:0008203cholesterol metabolic process0.00102675017073312
GO:0016125sterol metabolic process0.00102675017073312
GO:0004736pyruvate carboxylase activity0.00250629676560923
GO:0032810sterol response element binding0.00250629676560923
GO:0008202steroid metabolic process0.00250629676560923
GO:0032787monocarboxylic acid metabolic process0.00515569378181183
GO:0009374biotin binding0.00755915840589375
GO:0009267cellular response to starvation0.00944739489749404
GO:0019217regulation of fatty acid metabolic process0.00944739489749404
GO:0016885ligase activity, forming carbon-carbon bonds0.00944739489749404
GO:0031669cellular response to nutrient levels0.00944739489749404
GO:0015485cholesterol binding0.0100020277963888
GO:0042594response to starvation0.0100020277963888
GO:0031668cellular response to extracellular stimulus0.0100020277963888
GO:0019752carboxylic acid metabolic process0.0107367492345269
GO:0006082organic acid metabolic process0.0107367492345269
GO:0031667response to nutrient levels0.0122775759449278
GO:0032934sterol binding0.0123172879608904
GO:0031090organelle membrane0.0123172879608904
GO:0009991response to extracellular stimulus0.0123172879608904
GO:0033554cellular response to stress0.0128414179677663
GO:0006094gluconeogenesis0.0128414179677663
GO:0019216regulation of lipid metabolic process0.0137986537725932
GO:0051716cellular response to stimulus0.0139861729210222
GO:0006090pyruvate metabolic process0.0141602239531468
GO:0019319hexose biosynthetic process0.0147469997075971
GO:0005783endoplasmic reticulum0.0147469997075971
GO:0046165alcohol biosynthetic process0.0147469997075971
GO:0046364monosaccharide biosynthetic process0.0147469997075971
GO:0044444cytoplasmic part0.0163733969640664
GO:0005496steroid binding0.0260620613217157
GO:0005789endoplasmic reticulum membrane0.0376592756433307
GO:0042175nuclear envelope-endoplasmic reticulum network0.0381760376023527
GO:0016051carbohydrate biosynthetic process0.0396196000953267
GO:0044432endoplasmic reticulum part0.0396196000953267
GO:0006006glucose metabolic process0.0467633555420892
GO:0019842vitamin binding0.0493329562777339



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
exocrine gland8.32e-1225
exocrine system8.32e-1225
digestive tract diverticulum9.38e-1123
sac9.38e-1123
liver2.36e-1022
epithelial sac2.36e-1022
digestive gland2.36e-1022
epithelium of foregut-midgut junction2.36e-1022
anatomical boundary2.36e-1022
hepatobiliary system2.36e-1022
foregut-midgut junction2.36e-1022
hepatic diverticulum2.36e-1022
liver primordium2.36e-1022
septum transversum2.36e-1022
liver bud2.36e-1022
abdomen element5.05e-0949
abdominal segment element5.05e-0949
abdominal segment of trunk5.05e-0949
abdomen5.05e-0949
trunk mesenchyme1.75e-0845
trunk region element9.16e-0779


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)
MA0003.10.942378
MA0004.11.64673
MA0006.10.497533
MA0007.11.61215
MA0009.11.15569
MA0014.11.46333
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
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.11.35097
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.11.28762
MA0056.10
MA0057.11.29714
MA0058.11.4226
MA0059.10.59559
MA0060.12.74711
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
MA0073.10.216408
MA0074.10.795862
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
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.11.29026
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
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.11.24367
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
MA0145.10.21199
MA0146.10.647546
MA0147.11.15069
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.21.47117
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.21.0034
MA0047.20.845655
MA0112.20.211985
MA0065.20.609584
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.650923
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.346529
MA0163.11.64105
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.21.59291
MA0102.21.8929
MA0258.10.419871
MA0259.11.12353
MA0442.10
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