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MCL coexpression mm9:1258: Difference between revisions

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{{MCL_coexpression_mm9
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splicing;6.66597430610392e-06;56031,69878,67678,192170!GO:0006397;mRNA processing;1.23376633643291e-05;56031,69878,67678,192170!GO:0016071;mRNA metabolic process;1.45117378951032e-05;56031,69878,67678,192170!GO:0006396;RNA processing;4.03625053793264e-05;56031,69878,67678,192170!GO:0044428;nuclear part;4.39995964132779e-05;56031,69878,67678,192170,26572!GO:0030529;ribonucleoprotein complex;6.67731415176424e-05;56031,69878,67678,192170!GO:0030532;small nuclear ribonucleoprotein complex;6.67731415176424e-05;69878,67678!GO:0003723;RNA binding;0.000124435294817082;56031,69878,67678,192170!GO:0000375;RNA splicing, via transesterification reactions;0.000649988483381811;69878,67678!GO:0000398;nuclear mRNA splicing, via spliceosome;0.000649988483381811;69878,67678!GO:0000377;RNA splicing, via transesterification reactions with bulged adenosine as nucleophile;0.000649988483381811;69878,67678!GO:0032991;macromolecular complex;0.000649988483381811;56031,69878,67678,192170,26572!GO:0005634;nucleus;0.000769721621827877;56459,56031,69878,67678,192170,26572!GO:0044446;intracellular organelle part;0.00113519242690883;56031,69878,67678,192170,26572!GO:0044422;organelle part;0.00113519242690883;56031,69878,67678,192170,26572!GO:0030629;U6 snRNA 3'-end binding;0.00208829491364836;67678!GO:0017070;U6 snRNA binding;0.00394401676804148;67678!GO:0006374;nuclear mRNA splicing via U2-type spliceosome;0.00560388773734823;67678!GO:0043231;intracellular membrane-bound organelle;0.00739199319082538;56459,56031,69878,67678,192170,26572!GO:0043227;membrane-bound organelle;0.00739199319082538;56459,56031,69878,67678,192170,26572!GO:0004839;ubiquitin activating enzyme activity;0.00739199319082538;56459!GO:0017069;snRNA binding;0.00739199319082538;67678!GO:0046540;U4/U6 x U5 tri-snRNP complex;0.00739199319082538;67678!GO:0008641;small protein activating enzyme activity;0.0106270574167507;56459!GO:0043283;biopolymer metabolic process;0.0106270574167507;56459,56031,69878,67678,192170!GO:0016070;RNA metabolic process;0.0106270574167507;56031,69878,67678,192170!GO:0008180;signalosome;0.0113985425775183;26572!GO:0043229;intracellular organelle;0.0117543994217399;56459,56031,69878,67678,192170,26572!GO:0043226;organelle;0.0117543994217399;56459,56031,69878,67678,192170,26572!GO:0008022;protein C-terminus binding;0.0148630715030053;56459!GO:0005732;small nucleolar ribonucleoprotein complex;0.0166092194431962;69878!GO:0010467;gene expression;0.0166720700225567;56031,69878,67678,192170!GO:0000184;mRNA catabolic process, nonsense-mediated decay;0.0166720700225567;192170!GO:0003676;nucleic acid binding;0.0176196444999963;56031,69878,67678,192170!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0226282907447422;56031,69878,67678,192170!GO:0006402;mRNA catabolic process;0.0265999237757644;192170!GO:0043170;macromolecule metabolic process;0.0265999237757644;56459,56031,69878,67678,192170!GO:0044424;intracellular part;0.0265999237757644;56459,56031,69878,67678,192170,26572!GO:0006401;RNA catabolic process;0.0282804818424051;192170!GO:0003755;peptidyl-prolyl cis-trans isomerase activity;0.0289124408135589;56031!GO:0016859;cis-trans isomerase activity;0.0289124408135589;56031!GO:0044452;nucleolar part;0.0289124408135589;69878!GO:0005622;intracellular;0.0289124408135589;56459,56031,69878,67678,192170,26572!GO:0016567;protein ubiquitination;0.0298271027999113;56459!GO:0032446;protein modification by small protein conjugation;0.0345206046749659;56459!GO:0016072;rRNA metabolic process;0.0389208784610221;192170!GO:0006364;rRNA processing;0.0389208784610221;192170!GO:0044238;primary metabolic process;0.0410485133826842;56459,56031,69878,67678,192170!GO:0044237;cellular metabolic process;0.0410485133826842;56459,56031,69878,67678,192170!GO:0046982;protein heterodimerization 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|gostat_on_MCL_coexpression=GO:0005681;spliceosome;5.61954294543226e-06;56031,69878,67678,192170!GO:0008380;RNA splicing;6.66597430610392e-06;56031,69878,67678,192170!GO:0006397;mRNA processing;1.23376633643291e-05;56031,69878,67678,192170!GO:0016071;mRNA metabolic process;1.45117378951032e-05;56031,69878,67678,192170!GO:0006396;RNA processing;4.03625053793264e-05;56031,69878,67678,192170!GO:0044428;nuclear part;4.39995964132779e-05;56031,69878,67678,192170,26572!GO:0030529;ribonucleoprotein complex;6.67731415176424e-05;56031,69878,67678,192170!GO:0030532;small nuclear ribonucleoprotein complex;6.67731415176424e-05;69878,67678!GO:0003723;RNA binding;0.000124435294817082;56031,69878,67678,192170!GO:0000375;RNA splicing, via transesterification reactions;0.000649988483381811;69878,67678!GO:0000398;nuclear mRNA splicing, via spliceosome;0.000649988483381811;69878,67678!GO:0000377;RNA splicing, via transesterification reactions with bulged adenosine as nucleophile;0.000649988483381811;69878,67678!GO:0032991;macromolecular complex;0.000649988483381811;56031,69878,67678,192170,26572!GO:0005634;nucleus;0.000769721621827877;56459,56031,69878,67678,192170,26572!GO:0044446;intracellular organelle part;0.00113519242690883;56031,69878,67678,192170,26572!GO:0044422;organelle part;0.00113519242690883;56031,69878,67678,192170,26572!GO:0030629;U6 snRNA 3'-end binding;0.00208829491364836;67678!GO:0017070;U6 snRNA binding;0.00394401676804148;67678!GO:0006374;nuclear mRNA splicing via U2-type spliceosome;0.00560388773734823;67678!GO:0043231;intracellular membrane-bound organelle;0.00739199319082538;56459,56031,69878,67678,192170,26572!GO:0043227;membrane-bound organelle;0.00739199319082538;56459,56031,69878,67678,192170,26572!GO:0004839;ubiquitin activating enzyme activity;0.00739199319082538;56459!GO:0017069;snRNA binding;0.00739199319082538;67678!GO:0046540;U4/U6 x U5 tri-snRNP complex;0.00739199319082538;67678!GO:0008641;small protein activating enzyme activity;0.0106270574167507;56459!GO:0043283;biopolymer metabolic process;0.0106270574167507;56459,56031,69878,67678,192170!GO:0016070;RNA metabolic process;0.0106270574167507;56031,69878,67678,192170!GO:0008180;signalosome;0.0113985425775183;26572!GO:0043229;intracellular organelle;0.0117543994217399;56459,56031,69878,67678,192170,26572!GO:0043226;organelle;0.0117543994217399;56459,56031,69878,67678,192170,26572!GO:0008022;protein C-terminus binding;0.0148630715030053;56459!GO:0005732;small nucleolar ribonucleoprotein complex;0.0166092194431962;69878!GO:0010467;gene expression;0.0166720700225567;56031,69878,67678,192170!GO:0000184;mRNA catabolic process, nonsense-mediated decay;0.0166720700225567;192170!GO:0003676;nucleic acid binding;0.0176196444999963;56031,69878,67678,192170!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0226282907447422;56031,69878,67678,192170!GO:0006402;mRNA catabolic process;0.0265999237757644;192170!GO:0043170;macromolecule metabolic process;0.0265999237757644;56459,56031,69878,67678,192170!GO:0044424;intracellular part;0.0265999237757644;56459,56031,69878,67678,192170,26572!GO:0006401;RNA catabolic process;0.0282804818424051;192170!GO:0003755;peptidyl-prolyl cis-trans isomerase activity;0.0289124408135589;56031!GO:0016859;cis-trans isomerase activity;0.0289124408135589;56031!GO:0044452;nucleolar part;0.0289124408135589;69878!GO:0005622;intracellular;0.0289124408135589;56459,56031,69878,67678,192170,26572!GO:0016567;protein ubiquitination;0.0298271027999113;56459!GO:0032446;protein modification by small protein conjugation;0.0345206046749659;56459!GO:0016072;rRNA metabolic process;0.0389208784610221;192170!GO:0006364;rRNA processing;0.0389208784610221;192170!GO:0044238;primary metabolic process;0.0410485133826842;56459,56031,69878,67678,192170!GO:0044237;cellular metabolic process;0.0410485133826842;56459,56031,69878,67678,192170!GO:0046982;protein heterodimerization activity;0.0414298020721974;56459!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.473747,0.464605,0.535892,0.346849,0.550971,0.645383,1.28052,0.257202,0.594834,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.442204,0.426133,0.108444,2.67147,0.345236,0.472505,1.64218,0.223823,0.572827,0.394364,0.181062,0.558142,0.960397,0.336199,0.204204,0.364821,0.607065,0.871288,0.629145,0.820134,0.27383,0.342638,0.56353,0.0995018,0.366415,0.659176,0.524258,0.77511,0.589246,0.0835644,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,0.66551,0.406788,1.50238,0.614918,0.663395,0.939962,0.724164,0.269393,0.827522,1.62226,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.70565,0.740068,1.156,0.599223,0.57254,0.204132,1.80128,0.922432,0.430551,0.254777,0.874787,0.722675,0.676326,1.03903,0.198949,0.220054,0.534643,1.83587,1.77427,1.33021,1.04409,0.973447,0.35304,0.810643,0.281222,0.244935,0.976308,0.775372,0.938145,1.56871,0.960112,1.08669,0.839694,0.838613,0.563071,2.08158,0.585058,0.435642,1.09461,0.484547,1.0885,1.10269,1.47196,1.33732,0.340765,0.528609,2.29205,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.347287,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,0.540361,1.10885,1.10596,0.783181,0.678689,1.18867,1.70209,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,1.52669,0.895201
|tfbs_overrepresentation_jaspar=MA0003.1;0.476238,MA0004.1;1.3269,MA0006.1;0.359699,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.558098,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.969171,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.486223,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.0585191,MA0056.1;0,MA0057.1;0.149949,MA0058.1;1.11298,MA0059.1;1.99202,MA0060.1;0.757042,MA0061.1;0.307097,MA0063.1;0,MA0066.1;1.61836,MA0067.1;1.33603,MA0068.1;0.467569,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.000157319,MA0074.1;0.638014,MA0076.1;1.85013,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.111145,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;1.75322,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;0.398766,MA0105.1;0.199622,MA0106.1;0.737893,MA0107.1;0.392331,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.822296,MA0115.1;1.08851,MA0116.1;0.359483,MA0117.1;1.05576,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;0.682297,MA0140.1;0.625902,MA0141.1;1.07584,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;0.379391,MA0146.1;0.635245,MA0147.1;0.858298,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;4.14052,MA0035.2;0.630778,MA0039.2;0.769467,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;0.723439,MA0047.2;0.685741,MA0112.2;0.37938,MA0065.2;0.380324,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.159217,MA0155.1;0.414701,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.70356,MA0163.1;0.0423021,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.0912348,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.833237,MA0442.1;0
}}

Latest revision as of 16:38, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:93052366..93052426,-p1@Snrpf
Mm9::chr11:119161318..119161348,-p1@Eif4a3
Mm9::chr11:59653247..59653265,-p4@Cops3
Mm9::chr4:122817172..122817203,-p1@Ppie
Mm9::chr6:91466000..91466052,+p1@Lsm3
Mm9::chr7:16973106..16973122,-p2@Sae1


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:0005681spliceosome5.61954294543226e-06
GO:0008380RNA splicing6.66597430610392e-06
GO:0006397mRNA processing1.23376633643291e-05
GO:0016071mRNA metabolic process1.45117378951032e-05
GO:0006396RNA processing4.03625053793264e-05
GO:0044428nuclear part4.39995964132779e-05
GO:0030529ribonucleoprotein complex6.67731415176424e-05
GO:0030532small nuclear ribonucleoprotein complex6.67731415176424e-05
GO:0003723RNA binding0.000124435294817082
GO:0000375RNA splicing, via transesterification reactions0.000649988483381811
GO:0000398nuclear mRNA splicing, via spliceosome0.000649988483381811
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.000649988483381811
GO:0032991macromolecular complex0.000649988483381811
GO:0005634nucleus0.000769721621827877
GO:0044446intracellular organelle part0.00113519242690883
GO:0044422organelle part0.00113519242690883
GO:0030629U6 snRNA 3'-end binding0.00208829491364836
GO:0017070U6 snRNA binding0.00394401676804148
GO:0006374nuclear mRNA splicing via U2-type spliceosome0.00560388773734823
GO:0043231intracellular membrane-bound organelle0.00739199319082538
GO:0043227membrane-bound organelle0.00739199319082538
GO:0004839ubiquitin activating enzyme activity0.00739199319082538
GO:0017069snRNA binding0.00739199319082538
GO:0046540U4/U6 x U5 tri-snRNP complex0.00739199319082538
GO:0008641small protein activating enzyme activity0.0106270574167507
GO:0043283biopolymer metabolic process0.0106270574167507
GO:0016070RNA metabolic process0.0106270574167507
GO:0008180signalosome0.0113985425775183
GO:0043229intracellular organelle0.0117543994217399
GO:0043226organelle0.0117543994217399
GO:0008022protein C-terminus binding0.0148630715030053
GO:0005732small nucleolar ribonucleoprotein complex0.0166092194431962
GO:0010467gene expression0.0166720700225567
GO:0000184mRNA catabolic process, nonsense-mediated decay0.0166720700225567
GO:0003676nucleic acid binding0.0176196444999963
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0226282907447422
GO:0006402mRNA catabolic process0.0265999237757644
GO:0043170macromolecule metabolic process0.0265999237757644
GO:0044424intracellular part0.0265999237757644
GO:0006401RNA catabolic process0.0282804818424051
GO:0003755peptidyl-prolyl cis-trans isomerase activity0.0289124408135589
GO:0016859cis-trans isomerase activity0.0289124408135589
GO:0044452nucleolar part0.0289124408135589
GO:0005622intracellular0.0289124408135589
GO:0016567protein ubiquitination0.0298271027999113
GO:0032446protein modification by small protein conjugation0.0345206046749659
GO:0016072rRNA metabolic process0.0389208784610221
GO:0006364rRNA processing0.0389208784610221
GO:0044238primary metabolic process0.0410485133826842
GO:0044237cellular metabolic process0.0410485133826842
GO:0046982protein heterodimerization activity0.0414298020721974



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)
MA0003.10.476238
MA0004.11.3269
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.10.558098
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.969171
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.486223
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.149949
MA0058.11.11298
MA0059.11.99202
MA0060.10.757042
MA0061.10.307097
MA0063.10
MA0066.11.61836
MA0067.11.33603
MA0068.10.467569
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.000157319
MA0074.10.638014
MA0076.11.85013
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.111145
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.11.75322
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.822296
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.682297
MA0140.10.625902
MA0141.11.07584
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.379391
MA0146.10.635245
MA0147.10.858298
MA0148.10.553294
MA0149.10.464445
MA0062.24.14052
MA0035.20.630778
MA0039.20.769467
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.723439
MA0047.20.685741
MA0112.20.37938
MA0065.20.380324
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.414701
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.70356
MA0163.10.0423021
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.0912348
MA0102.21.7182
MA0258.10.290587
MA0259.10.833237
MA0442.10
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