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MCL coexpression mm9:1804: Difference between revisions

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{{MCL_coexpression_mm9
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of cell shape;0.0344235690782167;242481!GO:0022603;regulation of anatomical structure morphogenesis;0.0344235690782167;242481!GO:0022604;regulation of cell morphogenesis;0.0344235690782167;242481!GO:0005089;Rho guanyl-nucleotide exchange factor activity;0.0344235690782167;73341!GO:0035023;regulation of Rho protein signal transduction;0.0344235690782167;73341!GO:0005088;Ras guanyl-nucleotide exchange factor activity;0.0344235690782167;73341!GO:0007266;Rho protein signal transduction;0.0399849697541542;73341!GO:0046578;regulation of Ras protein signal transduction;0.0436795315613971;73341!GO:0005085;guanyl-nucleotide exchange factor activity;0.0436795315613971;73341!GO:0051056;regulation of small GTPase mediated signal transduction;0.0436795315613971;73341!GO:0007265;Ras protein signal transduction;0.0439393035088579;73341!GO:0005083;small GTPase regulator 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|gostat_on_MCL_coexpression=GO:0008360;regulation of cell shape;0.0344235690782167;242481!GO:0022603;regulation of anatomical structure morphogenesis;0.0344235690782167;242481!GO:0022604;regulation of cell morphogenesis;0.0344235690782167;242481!GO:0005089;Rho guanyl-nucleotide exchange factor activity;0.0344235690782167;73341!GO:0035023;regulation of Rho protein signal transduction;0.0344235690782167;73341!GO:0005088;Ras guanyl-nucleotide exchange factor activity;0.0344235690782167;73341!GO:0007266;Rho protein signal transduction;0.0399849697541542;73341!GO:0046578;regulation of Ras protein signal transduction;0.0436795315613971;73341!GO:0005085;guanyl-nucleotide exchange factor activity;0.0436795315613971;73341!GO:0051056;regulation of small GTPase mediated signal transduction;0.0436795315613971;73341!GO:0007265;Ras protein signal transduction;0.0439393035088579;73341!GO:0005083;small GTPase regulator activity;0.0439393035088579;73341!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007100!2.26e-11!18;UBERON:0000948!2.26e-11!18;UBERON:0005498!2.26e-11!18;UBERON:0004140!2.26e-11!18;UBERON:0009881!2.26e-11!18;UBERON:0004141!2.26e-11!18;UBERON:0003084!2.26e-11!18;UBERON:0007005!2.26e-11!18;UBERON:0004139!2.26e-11!18;UBERON:0004291!2.26e-11!18;UBERON:0004535!3.64e-10!23;UBERON:0001009!3.64e-10!23;UBERON:0002048!3.53e-08!14;UBERON:0000117!3.53e-08!14;UBERON:0000171!3.53e-08!14;UBERON:0000170!3.53e-08!14;UBERON:0005597!3.53e-08!14;UBERON:0000118!3.53e-08!14;UBERON:0005153!9.80e-08!17;UBERON:0005157!3.42e-07!20;UBERON:0004872!3.78e-07!33;UBERON:0000468!8.11e-07!333
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.612204,0.529553,1.46803,0.406364,0.618805,0.715644,0.300268,0.836099,1.78433,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.545768,0.489529,0.145201,0.727684,0.404661,0.537749,0.757752,0.274609,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,0.704734,0.425309,0.0566307,1.7724,0.699032,0.360612,0.328675,0.401916,0.631725,0.419293,0.426986,0.4934,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,2.07063,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.827208,4.38414,1.23259,2.03319,1.27178,0.253065,0.835925,0.997094,1.23692,1.50308,0.948899,0.794502,0.293164,1.1148,0.970369,0.618102,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,1.24825,0.491483,0.550229,1.16464,1.23956,0.674448,1.41481,0.399936,1.64321,0.607321,2.14787,0.991416,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,1.87987,1.14546,1.45154,1.3055,0.750642,1.43666,0.44142,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,3.78333,0.651755,1.93643,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,2.37965,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.0513167
}}

Latest revision as of 17:31, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr4:57580688..57580708,+p3@Palm2
Mm9::chr4:57580717..57580741,+p4@Palm2
Mm9::chr4:57580993..57581008,+p5@Palm2
Mm9::chr4:57581016..57581032,+p6@Palm2
Mm9::chrX:54579450..54579489,-p5@Arhgef6


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:0008360regulation of cell shape0.0344235690782167
GO:0022603regulation of anatomical structure morphogenesis0.0344235690782167
GO:0022604regulation of cell morphogenesis0.0344235690782167
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0344235690782167
GO:0035023regulation of Rho protein signal transduction0.0344235690782167
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0344235690782167
GO:0007266Rho protein signal transduction0.0399849697541542
GO:0046578regulation of Ras protein signal transduction0.0436795315613971
GO:0005085guanyl-nucleotide exchange factor activity0.0436795315613971
GO:0051056regulation of small GTPase mediated signal transduction0.0436795315613971
GO:0007265Ras protein signal transduction0.0439393035088579
GO:0005083small GTPase regulator activity0.0439393035088579



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
primary circulatory organ2.26e-1118
heart2.26e-1118
primitive heart tube2.26e-1118
primary heart field2.26e-1118
anterior lateral plate mesoderm2.26e-1118
heart tube2.26e-1118
heart primordium2.26e-1118
cardiac mesoderm2.26e-1118
cardiogenic plate2.26e-1118
heart rudiment2.26e-1118
cardiovascular system3.64e-1023
circulatory system3.64e-1023
lung3.53e-0814
respiratory tube3.53e-0814
respiration organ3.53e-0814
pair of lungs3.53e-0814
lung primordium3.53e-0814
lung bud3.53e-0814
epithelial bud9.80e-0817
epithelial fold3.42e-0720
splanchnic layer of lateral plate mesoderm3.78e-0733
multi-cellular organism8.11e-07333


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)
MA0003.11.79223
MA0004.12.50003
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.736185
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.13.72946
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.12.48306
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.28842
MA0056.10
MA0057.10.562607
MA0058.13.19314
MA0059.13.25322
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
MA0073.11.74609
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.453686
MA0089.10
MA0090.10.566938
MA0091.12.54547
MA0092.10.567278
MA0093.12.92084
MA0095.10
MA0098.10
MA0100.11.66135
MA0101.10.523409
MA0103.11.16573
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
MA0116.11.89177
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
MA0141.11.21195
MA0142.10.950155
MA0143.10.797553
MA0144.10.956957
MA0145.12.84353
MA0146.10.0604336
MA0147.13.60565
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.20.749235
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.24.17837
MA0047.20.75686
MA0112.20.47695
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.11.11105
MA0155.10.515751
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.245828
MA0163.10.0644585
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.21.7149
MA0102.21.79669
MA0258.10.346619
MA0259.11.71005
MA0442.10
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