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MCL coexpression mm9:1534: Difference between revisions

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{{MCL_coexpression_mm9
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activity;0.0140581485744978;51793!GO:0007263;nitric oxide mediated signal transduction;0.0140581485744978;51793!GO:0006527;arginine catabolic process;0.0140581485744978;51793!GO:0009065;glutamine family amino acid catabolic process;0.0140581485744978;51793!GO:0006525;arginine metabolic process;0.0140581485744978;51793!GO:0000051;urea cycle intermediate metabolic process;0.0140581485744978;51793!GO:0016813;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines;0.0144590175354349;51793!GO:0046209;nitric oxide metabolic process;0.0159295124047435;51793!GO:0006809;nitric oxide biosynthetic process;0.0159295124047435;51793!GO:0009064;glutamine family amino acid metabolic process;0.0252907999632458;51793!GO:0009063;amino acid catabolic process;0.0352383780418792;51793!GO:0009310;amine catabolic process;0.0360999982242433;51793!GO:0044270;nitrogen compound catabolic process;0.0360999982242433;51793!GO:0046982;protein heterodimerization activity;0.0360999982242433;!GO:0044271;nitrogen compound biosynthetic process;0.0426594836289343;51793!GO:0016810;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds;0.0473422454075528;51793!GO:0042803;protein homodimerization 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|gostat_on_MCL_coexpression=GO:0016403;dimethylargininase activity;0.0140581485744978;51793!GO:0007263;nitric oxide mediated signal transduction;0.0140581485744978;51793!GO:0006527;arginine catabolic process;0.0140581485744978;51793!GO:0009065;glutamine family amino acid catabolic process;0.0140581485744978;51793!GO:0006525;arginine metabolic process;0.0140581485744978;51793!GO:0000051;urea cycle intermediate metabolic process;0.0140581485744978;51793!GO:0016813;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines;0.0144590175354349;51793!GO:0046209;nitric oxide metabolic process;0.0159295124047435;51793!GO:0006809;nitric oxide biosynthetic process;0.0159295124047435;51793!GO:0009064;glutamine family amino acid metabolic process;0.0252907999632458;51793!GO:0009063;amino acid catabolic process;0.0352383780418792;51793!GO:0009310;amine catabolic process;0.0360999982242433;51793!GO:0044270;nitrogen compound catabolic process;0.0360999982242433;51793!GO:0046982;protein heterodimerization activity;0.0360999982242433;!GO:0044271;nitrogen compound biosynthetic process;0.0426594836289343;51793!GO:0016810;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds;0.0473422454075528;51793!GO:0042803;protein homodimerization activity;0.0499882081296951;!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.557864,2.0905,0.529553,1.46803,1.04755,0.618805,0.715644,0.300268,2.30336,1.78433,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.185796,0.489529,0.874994,1.72742,0.404661,0.537749,0.757752,0.274609,0.641282,1.15581,0.645258,0.626183,1.03545,0.395107,0.253145,0.425309,0.20704,0.384813,0.699032,0.360612,0.876199,0.401916,0.631725,0.134724,1.09239,2.97127,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,2.88731,0.734051,1.01481,1.86856,0.323911,0.901018,1.76944,0.943088,1.33705,1.68977,2.30638,1.54147,0.509047,0.30684,1.45025,1.23259,0.257421,1.27178,0.253065,0.835925,0.997094,1.23692,0.308173,0.948899,0.794502,0.293164,1.1148,1.99513,0.0882907,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.937248,0.3366,0.806207,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,1.35621,1.16464,0.495367,0.674448,1.41481,0.399936,0.673306,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,1.06895,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,1.39694,1.85301,0.651755,0.826123,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.0513167
|tfbs_overrepresentation_jaspar=MA0003.1;0.406907,MA0004.1;0.603793,MA0006.1;0.419915,MA0007.1;6.11457,MA0009.1;1.06266,MA0014.1;3.30772,MA0017.1;0.449113,MA0019.1;0.874061,MA0024.1;1.01759,MA0025.1;1.30092,MA0027.1;2.72141,MA0028.1;0.43138,MA0029.1;0.995171,MA0030.1;1.00195,MA0031.1;0.965177,MA0038.1;0.757669,MA0040.1;1.07552,MA0041.1;0.522007,MA0042.1;0.507715,MA0043.1;1.1618,MA0046.1;1.09955,MA0048.1;0.205696,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;0.0851423,MA0056.1;0,MA0057.1;0.192781,MA0058.1;0.50032,MA0059.1;0.513699,MA0060.1;0.330907,MA0061.1;0.364227,MA0063.1;0,MA0066.1;2.95375,MA0067.1;1.41352,MA0068.1;1.71065,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;0.310158,MA0074.1;0.708108,MA0076.1;0.470037,MA0077.1;1.04318,MA0078.1;1.88054,MA0081.1;0.53877,MA0083.1;1.16099,MA0084.1;1.74401,MA0087.1;1.11687,MA0088.1;0.148348,MA0089.1;0,MA0090.1;0.566938,MA0091.1;0.617887,MA0092.1;1.39225,MA0093.1;0.440484,MA0095.1;0,MA0098.1;0,MA0100.1;0.695835,MA0101.1;0.523409,MA0103.1;0.460936,MA0105.1;0.248108,MA0106.1;0.809991,MA0107.1;0.454197,MA0108.2;0.897859,MA0109.1;0,MA0111.1;0.582193,MA0113.1;0.780358,MA0114.1;0.361633,MA0115.1;1.16466,MA0116.1;0.419688,MA0117.1;1.13165,MA0119.1;0.524046,MA0122.1;1.15196,MA0124.1;1.35963,MA0125.1;1.28445,MA0130.1;0,MA0131.1;0.869325,MA0132.1;0,MA0133.1;0,MA0135.1;1.19898,MA0136.1;0.729175,MA0139.1;0.295945,MA0140.1;0.695713,MA0141.1;0.482463,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;0.157686,MA0146.1;2.29697,MA0147.1;0.986917,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;10.7493,MA0138.2;0.861035,MA0002.2;0.299191,MA0137.2;2.09225,MA0104.2;0.845917,MA0047.2;0.75686,MA0112.2;6.27451,MA0065.2;0.158101,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;1.74374,MA0155.1;0.99229,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;1.01146,MA0160.1;0.624415,MA0161.1;0,MA0162.1;2.45609,MA0163.1;0.230013,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;5.98237,MA0102.2;1.79669,MA0258.1;4.41789,MA0259.1;1.71005,MA0442.1;0
}}

Latest revision as of 17:05, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:79896129..79896163,-p6@Tcf3
Mm9::chr17:35195986..35196075,+p1@Ddah2
Mm9::chr17:35196090..35196101,+p4@Ddah2
Mm9::chr17:35196103..35196114,+p3@Ddah2
Mm9::chr17:35196118..35196133,+p2@Ddah2


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:0016403dimethylargininase activity0.0140581485744978
GO:0007263nitric oxide mediated signal transduction0.0140581485744978
GO:0006527arginine catabolic process0.0140581485744978
GO:0009065glutamine family amino acid catabolic process0.0140581485744978
GO:0006525arginine metabolic process0.0140581485744978
GO:0000051urea cycle intermediate metabolic process0.0140581485744978
GO:0016813hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines0.0144590175354349
GO:0046209nitric oxide metabolic process0.0159295124047435
GO:0006809nitric oxide biosynthetic process0.0159295124047435
GO:0009064glutamine family amino acid metabolic process0.0252907999632458
GO:0009063amino acid catabolic process0.0352383780418792
GO:0009310amine catabolic process0.0360999982242433
GO:0044270nitrogen compound catabolic process0.0360999982242433
GO:0046982protein heterodimerization activity0.0360999982242433
GO:0044271nitrogen compound biosynthetic process0.0426594836289343
GO:0016810hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.0473422454075528
GO:0042803protein homodimerization activity0.0499882081296951



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>cell_data<br><br><br>

Cell Type
Ontology termp-valuen
ectodermal cell1.71e-1044
neurectodermal cell1.71e-1044
neural cell5.80e-1043
non-terminally differentiated cell5.88e-0949
neuron1.25e-0733
neuronal stem cell1.25e-0733
neuroblast1.25e-0733
electrically signaling cell1.25e-0733


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)
MA0003.10.406907
MA0004.10.603793
MA0006.10.419915
MA0007.16.11457
MA0009.11.06266
MA0014.13.30772
MA0017.10.449113
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
MA0055.10.0851423
MA0056.10
MA0057.10.192781
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.10.364227
MA0063.10
MA0066.12.95375
MA0067.11.41352
MA0068.11.71065
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.310158
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.11.88054
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.148348
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.11.39225
MA0093.10.440484
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
MA0145.10.157686
MA0146.12.29697
MA0147.10.986917
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.210.7493
MA0138.20.861035
MA0002.20.299191
MA0137.22.09225
MA0104.20.845917
MA0047.20.75686
MA0112.26.27451
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.11.74374
MA0155.10.99229
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.11.01146
MA0160.10.624415
MA0161.10
MA0162.12.45609
MA0163.10.230013
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.25.98237
MA0102.21.79669
MA0258.14.41789
MA0259.11.71005
MA0442.10
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