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MCL coexpression mm9:1752: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!1.53e-08!47;UBERON:0005256!1.79e-08!45;UBERON:0002365!5.93e-08!25;UBERON:0002330!5.93e-08!25;UBERON:0003104!1.01e-07!61;UBERON:0009142!1.01e-07!61
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.293744,0.529553,1.46803,0.406364,0.618805,0.715644,0.812379,0.310789,0.370407,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,1.02841,0.283802,0.185796,0.489529,0.874994,0.727684,0.404661,0.537749,0.757752,0.274609,0.641282,0.456327,0.227599,0.626183,1.03545,0.395107,0.253145,3.88391,0.454919,0.384813,0.699032,0.360612,0.328675,1.03785,0.631725,0.419293,0.426986,1.78875,0.591277,0.847828,0.658142,0.370501,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,1.74508,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.152094,1.23259,0.714607,2.75658,0.253065,0.835925,0.997094,0.494135,0.830212,0.948899,0.794502,1.44895,1.1148,0.574099,0.0882907,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,1.7727,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,1.61686,1.41481,1.03353,2.24107,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,1.77493,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,0.133815,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,9.64626
}}

Latest revision as of 17:26, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:52901876..52901906,+p1@Hibch
Mm9::chr1:52901915..52901938,+p2@Hibch
Mm9::chr1:52901943..52901954,+p4@Hibch
Mm9::chr6:136610198..136610212,-p7@Plbd1
Mm9::chr6:145159661..145159742,+p1@Lyrm5


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:00038603-hydroxyisobutyryl-CoA hydrolase activity0.00169835095600723
GO:0009083branched chain family amino acid catabolic process0.00396281889735021
GO:0009081branched chain family amino acid metabolic process0.00396281889735021
GO:0016289CoA hydrolase activity0.00679340382402893
GO:0009063amino acid catabolic process0.0135868076480579
GO:0009310amine catabolic process0.0135868076480579
GO:0044270nitrogen compound catabolic process0.0135868076480579
GO:0016790thiolester hydrolase activity0.0186818605160796
GO:0006520amino acid metabolic process0.0403830116206164
GO:0006519amino acid and derivative metabolic process0.047893496959404
GO:0009308amine metabolic process0.0499598239558794
GO:0006807nitrogen compound metabolic process0.0499598239558794



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 tube1.53e-0847
trunk mesenchyme1.79e-0845
exocrine gland5.93e-0825
exocrine system5.93e-0825
mesenchyme1.01e-0761
entire embryonic mesenchyme1.01e-0761


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)
MA0003.10.6678
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.13.97269
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.11.10192
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
MA0048.10.593503
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.13.36884
MA0056.10
MA0057.10.192781
MA0058.10.50032
MA0059.10.513699
MA0060.10.881183
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
MA0073.10.189951
MA0074.10.708108
MA0076.12.06136
MA0077.11.04318
MA0078.10.801834
MA0081.11.33193
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.148348
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.11.12162
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.10.524046
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
MA0144.10.365053
MA0145.10.927481
MA0146.11.74263
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.22.01551
MA0035.20.700704
MA0039.29.18769
MA0138.20.861035
MA0002.21.47075
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.47695
MA0065.20.477991
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.12.72392
MA0154.10.203217
MA0155.11.57585
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.13.09272
MA0163.10.497328
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.21.19329
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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