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MCL coexpression mm9:1499: Difference between revisions

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{{MCL_coexpression_mm9
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binding;5.96824109179168e-05;20115,66870,18813!GO:0042254;ribosome biogenesis and assembly;5.96824109179168e-05;20115,18813!GO:0022613;ribonucleoprotein complex biogenesis and assembly;0.000141697525165298;20115,18813!GO:0016072;rRNA metabolic process;0.000911051986071722;18813!GO:0006364;rRNA processing;0.000911051986071722;18813!GO:0030529;ribonucleoprotein complex;0.000911051986071722;20115,18813!GO:0001651;dense fibrillar component;0.003067988823755;!GO:0030515;snoRNA binding;0.0053356630978383;!GO:0003676;nucleic acid binding;0.0053356630978383;20115,66870,18813!GO:0006996;organelle organization and biogenesis;0.00814978272683597;20115,18813!GO:0004239;methionyl aminopeptidase activity;0.00975857397116205;18813!GO:0006396;RNA processing;0.0172167034609127;18813!GO:0050897;cobalt ion binding;0.0181570045119305;18813!GO:0005843;cytosolic small ribosomal subunit (sensu Eukaryota);0.0201105226744863;20115!GO:0006412;translation;0.0201105226744863;20115,18813!GO:0005732;small nucleolar 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|ontology_enrichment_disease=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.293744,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.836099,0.370407,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.545768,0.489529,0.44579,0.727684,0.404661,0.537749,0.757752,0.274609,0.641282,1.15581,0.227599,1.51608,1.03545,0.395107,0.253145,0.425309,0.20704,1.00043,0.699032,0.360612,0.876199,0.401916,0.631725,0.134724,1.09239,0.0637209,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,1.17664,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,3.55898,1.23259,0.714607,0.245132,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.796301,1.1148,0.970369,0.297068,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,2.52449,0.3366,0.297538,1.05152,0.848095,1.75016,0.384901,1.03517,1.16282,0.913356,2.10706,0.631253,0.97421,0.653843,1.24825,1.23125,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.673306,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.651755,2.6072,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.425122
|tfbs_overrepresentation_jaspar=MA0003.1;0.211284,MA0004.1;0.603793,MA0006.1;0.419915,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;0.187732,MA0017.1;0.449113,MA0019.1;0.874061,MA0024.1;1.01759,MA0025.1;1.30092,MA0027.1;2.72141,MA0028.1;3.91962,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;1.55615,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;0.28842,MA0056.1;0,MA0057.1;0.192781,MA0058.1;0.50032,MA0059.1;1.27866,MA0060.1;0.330907,MA0061.1;0.364227,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;1.08757,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;0.103695,MA0074.1;0.708108,MA0076.1;4.14461,MA0077.1;1.04318,MA0078.1;0.801834,MA0081.1;0.53877,MA0083.1;1.16099,MA0084.1;1.74401,MA0087.1;1.11687,MA0088.1;2.75276,MA0089.1;0,MA0090.1;0.566938,MA0091.1;0.617887,MA0092.1;0.567278,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;1.07655,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;0.476962,MA0146.1;0.475727,MA0147.1;0.378658,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;3.69273,MA0035.2;0.700704,MA0039.2;0.0511423,MA0138.2;0.861035,MA0002.2;0.299191,MA0137.2;0.479301,MA0104.2;0.845917,MA0047.2;0.75686,MA0112.2;0.157681,MA0065.2;0.158101,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;0.203217,MA0155.1;0.173445,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;1.01146,MA0160.1;0.624415,MA0161.1;0,MA0162.1;0.526186,MA0163.1;0.230013,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;0.130118,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;0.366802,MA0442.1;0
}}

Latest revision as of 17:02, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128002960..128003055,-p1@Pa2g4
Mm9::chr12:29320756..29320770,-p4@Rps7
Mm9::chr1:144991185..144991219,-p@chr1:144991185..144991219
-
Mm9::chr3:129534041..129534104,-p1@Gar1
Mm9::chr6:67216981..67217015,+p1@Serbp1


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:0003723RNA binding5.96824109179168e-05
GO:0042254ribosome biogenesis and assembly5.96824109179168e-05
GO:0022613ribonucleoprotein complex biogenesis and assembly0.000141697525165298
GO:0016072rRNA metabolic process0.000911051986071722
GO:0006364rRNA processing0.000911051986071722
GO:0030529ribonucleoprotein complex0.000911051986071722
GO:0001651dense fibrillar component0.003067988823755
GO:0030515snoRNA binding0.0053356630978383
GO:0003676nucleic acid binding0.0053356630978383
GO:0006996organelle organization and biogenesis0.00814978272683597
GO:0004239methionyl aminopeptidase activity0.00975857397116205
GO:0006396RNA processing0.0172167034609127
GO:0050897cobalt ion binding0.0181570045119305
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.0201105226744863
GO:0006412translation0.0201105226744863
GO:0005732small nucleolar ribonucleoprotein complex0.0201105226744863
GO:0032991macromolecular complex0.0263349046740459
GO:0019843rRNA binding0.0273918789093124
GO:0015935small ribosomal subunit0.0338286166136434
GO:0009059macromolecule biosynthetic process0.0343384152329058
GO:0016043cellular component organization and biogenesis0.0343384152329058
GO:0044452nucleolar part0.0344461389135031
GO:0004177aminopeptidase activity0.0344461389135031
GO:0005830cytosolic ribosome (sensu Eukaryota)0.0427862167485571
GO:0010467gene expression0.042860735323676
GO:0044249cellular biosynthetic process0.043553479040313
GO:0008235metalloexopeptidase activity0.043553479040313
GO:0033279ribosomal subunit0.0473159543949282



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><br><br>


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)
MA0003.10.211284
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.187732
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.13.91962
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
MA0050.11.55615
MA0051.10.767098
MA0052.11.08379
MA0055.10.28842
MA0056.10
MA0057.10.192781
MA0058.10.50032
MA0059.11.27866
MA0060.10.330907
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.11.08757
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.103695
MA0074.10.708108
MA0076.14.14461
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.12.75276
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
MA0105.10.248108
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.11.07655
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
MA0145.10.476962
MA0146.10.475727
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.23.69273
MA0035.20.700704
MA0039.20.0511423
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.845917
MA0047.20.75686
MA0112.20.157681
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.173445
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.11.01146
MA0160.10.624415
MA0161.10
MA0162.10.526186
MA0163.10.230013
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.130118
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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