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MCL coexpression mm9:1832: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0051786;all-trans-retinol 13,14-reductase activity;0.00383467085990169;67442!GO:0042572;retinol metabolic process;0.00383467085990169;67442!GO:0016117;carotenoid biosynthetic process;0.00383467085990169;67442!GO:0016114;terpenoid biosynthetic process;0.00383467085990169;67442!GO:0005640;nuclear outer membrane;0.00383467085990169;67442!GO:0016109;tetraterpenoid biosynthetic process;0.00383467085990169;67442!GO:0016116;carotenoid metabolic process;0.00383467085990169;67442!GO:0016108;tetraterpenoid metabolic process;0.00383467085990169;67442!GO:0001523;retinoid metabolic process;0.00920119297709492;67442!GO:0016101;diterpenoid metabolic process;0.00920119297709492;67442!GO:0006721;terpenoid metabolic process;0.00975830620272628;67442!GO:0006776;vitamin A metabolic process;0.0100255672477407;67442!GO:0008299;isoprenoid biosynthetic process;0.0100255672477407;67442!GO:0031968;organelle outer membrane;0.0112428208673715;67442!GO:0006775;fat-soluble vitamin metabolic process;0.0112428208673715;67442!GO:0046148;pigment biosynthetic process;0.0124551687479699;67442!GO:0006720;isoprenoid metabolic process;0.0130740339887141;67442!GO:0042440;pigment metabolic process;0.0131985404761078;67442!GO:0016627;oxidoreductase activity, acting on the CH-CH group of donors;0.0164714667062015;67442!GO:0019748;secondary metabolic process;0.0164714667062015;67442!GO:0019867;outer membrane;0.0167801800199425;67442!GO:0050660;FAD binding;0.0192955015041163;67442!GO:0044453;nuclear membrane part;0.0192955015041163;67442!GO:0006766;vitamin metabolic process;0.0192955015041163;67442!GO:0031965;nuclear membrane;0.0192955015041163;67442!GO:0005789;endoplasmic reticulum membrane;0.0206108922087199;67442!GO:0042175;nuclear envelope-endoplasmic reticulum network;0.0206964298290346;67442!GO:0044432;endoplasmic reticulum part;0.0213760759761628;67442!GO:0042445;hormone metabolic process;0.0213760759761628;67442!GO:0005635;nuclear envelope;0.0275309638111959;67442!GO:0050662;coenzyme binding;0.0286101241571493;67442!GO:0016705;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;0.0298590547782988;67442!GO:0048037;cofactor binding;0.0388684960662591;67442!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005256!3.31e-07!45;UBERON:0003104!4.07e-07!61;UBERON:0009142!4.07e-07!61;UBERON:0009854!8.09e-07!23;UBERON:0009856!8.09e-07!23
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.293744,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,1.51246,0.746305,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,1.41491,0.545768,0.489529,0.874994,0.727684,0.404661,1.32977,0.757752,0.274609,0.641282,0.456327,0.227599,0.626183,1.03545,0.395107,0.253145,0.425309,0.20704,0.384813,1.66799,0.947152,0.328675,0.401916,0.631725,0.830062,0.426986,1.28479,0.591277,0.847828,0.658142,0.370501,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,1.74508,0.469329,0.689304,1.34464,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.152094,1.23259,0.257421,1.27178,0.70455,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,0.574099,0.0882907,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,1.06179,0.356133,0.3366,0.297538,1.05152,0.848095,0.590368,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,1.23125,1.35621,1.16464,0.495367,0.674448,1.41481,0.399936,0.673306,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,1.45154,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.651755,0.133815,1.18223,0.908552,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.997706,0.701187,0.745913
}}

Latest revision as of 17:34, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr6:72548588..72548603,+p1@Retsat
Mm9::chr7:105499448..105499454,-p@chr7:105499448..105499454
-
Mm9::chr7:105508945..105508980,-p5@Tsku
Mm9::chr7:105509758..105509765,-p4@Tsku
Mm9::chr7:105509785..105509805,-p1@Tsku


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:0051786all-trans-retinol 13,14-reductase activity0.00383467085990169
GO:0042572retinol metabolic process0.00383467085990169
GO:0016117carotenoid biosynthetic process0.00383467085990169
GO:0016114terpenoid biosynthetic process0.00383467085990169
GO:0005640nuclear outer membrane0.00383467085990169
GO:0016109tetraterpenoid biosynthetic process0.00383467085990169
GO:0016116carotenoid metabolic process0.00383467085990169
GO:0016108tetraterpenoid metabolic process0.00383467085990169
GO:0001523retinoid metabolic process0.00920119297709492
GO:0016101diterpenoid metabolic process0.00920119297709492
GO:0006721terpenoid metabolic process0.00975830620272628
GO:0006776vitamin A metabolic process0.0100255672477407
GO:0008299isoprenoid biosynthetic process0.0100255672477407
GO:0031968organelle outer membrane0.0112428208673715
GO:0006775fat-soluble vitamin metabolic process0.0112428208673715
GO:0046148pigment biosynthetic process0.0124551687479699
GO:0006720isoprenoid metabolic process0.0130740339887141
GO:0042440pigment metabolic process0.0131985404761078
GO:0016627oxidoreductase activity, acting on the CH-CH group of donors0.0164714667062015
GO:0019748secondary metabolic process0.0164714667062015
GO:0019867outer membrane0.0167801800199425
GO:0050660FAD binding0.0192955015041163
GO:0044453nuclear membrane part0.0192955015041163
GO:0006766vitamin metabolic process0.0192955015041163
GO:0031965nuclear membrane0.0192955015041163
GO:0005789endoplasmic reticulum membrane0.0206108922087199
GO:0042175nuclear envelope-endoplasmic reticulum network0.0206964298290346
GO:0044432endoplasmic reticulum part0.0213760759761628
GO:0042445hormone metabolic process0.0213760759761628
GO:0005635nuclear envelope0.0275309638111959
GO:0050662coenzyme binding0.0286101241571493
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.0298590547782988
GO:0048037cofactor binding0.0388684960662591



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 mesenchyme3.31e-0745
mesenchyme4.07e-0761
entire embryonic mesenchyme4.07e-0761
digestive tract diverticulum8.09e-0723
sac8.09e-0723


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)
MA0003.11.36559
MA0004.10.603793
MA0006.10.419915
MA0007.11.43525
MA0009.11.06266
MA0014.11.13011
MA0017.11.14026
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.11.50466
MA0056.10
MA0057.11.06992
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.103695
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.11.42769
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.11.28296
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.949408
MA0115.11.16466
MA0116.11.07655
MA0117.11.13165
MA0119.11.30068
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.295945
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.956957
MA0145.10.927481
MA0146.10.475727
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.20.489701
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.157681
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.12.46536
MA0155.10.515751
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.0699535
MA0163.10.230013
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.435944
MA0102.21.79669
MA0258.10.346619
MA0259.10.960816
MA0442.10
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