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MCL coexpression mm9:642: Difference between revisions

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{{MCL_coexpression_mm9
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ribosome (sensu Eukaryota);9.557703969472e-07;19989,20102,20091!GO:0044445;cytosolic part;3.70361028817039e-06;19989,20102,20091!GO:0042254;ribosome biogenesis and assembly;5.71244485397111e-06;19989,20102,20091!GO:0003735;structural constituent of ribosome;7.83096239860434e-06;19989,20102,20091!GO:0005840;ribosome;7.83096239860434e-06;19989,20102,20091!GO:0022613;ribonucleoprotein complex biogenesis and assembly;1.01992129043795e-05;19989,20102,20091!GO:0005829;cytosol;4.99082788914681e-05;19989,20102,20091!GO:0006412;translation;8.83646829602944e-05;19989,20102,20091!GO:0030529;ribonucleoprotein complex;8.83646829602944e-05;19989,20102,20091!GO:0033279;ribosomal subunit;0.000190297560796954;19989,20102!GO:0009059;macromolecule biosynthetic process;0.000218456752708339;19989,20102,20091!GO:0044249;cellular biosynthetic process;0.000454896551631285;19989,20102,20091!GO:0006996;organelle organization and biogenesis;0.000937821005258417;19989,20102,20091!GO:0009058;biosynthetic 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|gostat_on_MCL_coexpression=GO:0005830;cytosolic ribosome (sensu Eukaryota);9.557703969472e-07;19989,20102,20091!GO:0044445;cytosolic part;3.70361028817039e-06;19989,20102,20091!GO:0042254;ribosome biogenesis and assembly;5.71244485397111e-06;19989,20102,20091!GO:0003735;structural constituent of ribosome;7.83096239860434e-06;19989,20102,20091!GO:0005840;ribosome;7.83096239860434e-06;19989,20102,20091!GO:0022613;ribonucleoprotein complex biogenesis and assembly;1.01992129043795e-05;19989,20102,20091!GO:0005829;cytosol;4.99082788914681e-05;19989,20102,20091!GO:0006412;translation;8.83646829602944e-05;19989,20102,20091!GO:0030529;ribonucleoprotein complex;8.83646829602944e-05;19989,20102,20091!GO:0033279;ribosomal subunit;0.000190297560796954;19989,20102!GO:0009059;macromolecule biosynthetic process;0.000218456752708339;19989,20102,20091!GO:0044249;cellular biosynthetic process;0.000454896551631285;19989,20102,20091!GO:0006996;organelle organization and biogenesis;0.000937821005258417;19989,20102,20091!GO:0009058;biosynthetic process;0.000966962585761618;19989,20102,20091!GO:0043232;intracellular non-membrane-bound organelle;0.0017987821946727;19989,20102,20091!GO:0043228;non-membrane-bound organelle;0.0017987821946727;19989,20102,20091!GO:0032991;macromolecular complex;0.00409170790312737;19989,20102,20091!GO:0016043;cellular component organization and biogenesis;0.00632335480551472;19989,20102,20091!GO:0005843;cytosolic small ribosomal subunit (sensu Eukaryota);0.00677704069835615;20102!GO:0003723;RNA binding;0.00703688467131023;19989,20102!GO:0044267;cellular protein metabolic process;0.00746877384961488;19989,20102,20091!GO:0044260;cellular macromolecule metabolic process;0.00746877384961488;19989,20102,20091!GO:0010467;gene expression;0.00746877384961488;19989,20102,20091!GO:0019538;protein metabolic process;0.00766292771031945;19989,20102,20091!GO:0019843;rRNA binding;0.00845744660960953;20102!GO:0044444;cytoplasmic part;0.0101197450132424;19989,20102,20091!GO:0015935;small ribosomal subunit;0.0102103889682027;20102!GO:0015934;large ribosomal subunit;0.0105009629883662;19989!GO:0005737;cytoplasm;0.0463808671729333;19989,20102,20091!GO:0043170;macromolecule metabolic process;0.0463808671729333;19989,20102,20091!
|ontology_enrichment_celltype=CL:0000548!3.25e-08!115;CL:0000255!3.25e-08!115;CL:0000034!4.16e-08!97;CL:0002371!4.72e-08!118
|ontology_enrichment_disease=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.795069,0.286791,0.269904,0.329881,0.176699,0.342839,0.425757,0.702429,0.362206,0.660314,1.00157,0.414631,0.345518,0.437133,0.189961,0,0.619876,0.170475,0.318616,0.171249,0.238546,0.281622,1.11256,0.520732,0.758244,0.4628,0.0908349,0.949712,0.611503,0.231659,0.349031,0.717576,0.168723,0.965283,0.556756,0.497128,1.50631,1.0583,0.445168,0.391645,0.51597,0.931853,0.255102,0.191571,0.195622,0.856658,0.543674,0.376103,0.401883,0.61724,0.603113,1.22385,0.479906,0.855661,0.87275,0.443782,0.223087,1.03993,0.0851299,1.9669,0.698157,1.24284,0.120887,0.592318,2.98364,0.631188,1.00675,1.3527,0.693631,1.20659,0.253722,0.355763,1.25712,0.905636,0.277092,0.258161,0.270351,1.31942,0.681539,0.242107,0.357936,0.636582,0.495545,0.682423,0.792744,0.444993,0.0525502,0.0651072,0.548334,1.51408,1.07554,0.797601,0.730003,0.181374,0.437593,0.404817,1.14799,0.732731,0.543917,0.437273,0.943642,0.717305,0.838603,0.603683,0.602672,0.930972,0.660145,0.973236,0.246223,0.240055,0.286453,0.840348,0.681364,1.79049,1.0825,0.986944,0.170188,0.333247,2.5559,0.158673,0.910937,0.572279,0.464505,0.532013,1.13603,0.685116,0.433317,0.723425,1.00525,0.183744,0.821997,1.55739,0.976125,0.456508,1.10385,1.19208,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,0.178088,0.0664621,0.765699,0.857198,0.133365,0.455644,0.93735,0.488969,0.199652,0.290467,0.811219,1.06466,0.791909,0.685546,0.776587,0.593295,0.448733,0.160658,0.413167,0.671583
}}

Latest revision as of 15:39, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:79755159..79755181,+p2@LOC100046223
p2@Rps15
Mm9::chr15:5066589..5066629,+p2@Gm13826
p2@Rpl37
Mm9::chr1:16094477..16094516,-p1@Rpl7
Mm9::chr1:39424661..39424693,+p2@Gm10191
p2@Gm13004
p2@Gm7689
p2@Gm8759
p2@LOC100505081
p2@LOC638399
p2@Rpl31
Mm9::chr1:72757812..72757826,+p2@Gm14173
p2@Rpl37a
Mm9::chr2:26766267..26766289,+p2@Gm11362
p2@Rpl7a
Mm9::chr3:85946515..85946558,-p1@Rps3a
Mm9::chr5:121654486..121654508,+p2@Gm6136
p2@Rpl6
Mm9::chr7:25669587..25669626,+p1@Rps19-ps4
p1@Rps19-ps6
p1@Rps19
Mm9::chr9:106331730..106331788,+p2@Gm10913
p2@Gm13141
p2@Gm13841
p2@Gm6344
p2@Gm6887
p2@Gm8210
p2@Rpl29
Mm9::chrX:99384678..99384703,-p2@Rps4x


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:0005830cytosolic ribosome (sensu Eukaryota)9.557703969472e-07
GO:0044445cytosolic part3.70361028817039e-06
GO:0042254ribosome biogenesis and assembly5.71244485397111e-06
GO:0003735structural constituent of ribosome7.83096239860434e-06
GO:0005840ribosome7.83096239860434e-06
GO:0022613ribonucleoprotein complex biogenesis and assembly1.01992129043795e-05
GO:0005829cytosol4.99082788914681e-05
GO:0006412translation8.83646829602944e-05
GO:0030529ribonucleoprotein complex8.83646829602944e-05
GO:0033279ribosomal subunit0.000190297560796954
GO:0009059macromolecule biosynthetic process0.000218456752708339
GO:0044249cellular biosynthetic process0.000454896551631285
GO:0006996organelle organization and biogenesis0.000937821005258417
GO:0009058biosynthetic process0.000966962585761618
GO:0043232intracellular non-membrane-bound organelle0.0017987821946727
GO:0043228non-membrane-bound organelle0.0017987821946727
GO:0032991macromolecular complex0.00409170790312737
GO:0016043cellular component organization and biogenesis0.00632335480551472
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.00677704069835615
GO:0003723RNA binding0.00703688467131023
GO:0044267cellular protein metabolic process0.00746877384961488
GO:0044260cellular macromolecule metabolic process0.00746877384961488
GO:0010467gene expression0.00746877384961488
GO:0019538protein metabolic process0.00766292771031945
GO:0019843rRNA binding0.00845744660960953
GO:0044444cytoplasmic part0.0101197450132424
GO:0015935small ribosomal subunit0.0102103889682027
GO:0015934large ribosomal subunit0.0105009629883662
GO:0005737cytoplasm0.0463808671729333
GO:0043170macromolecule metabolic process0.0463808671729333



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
animal cell3.25e-08115
eukaryotic cell3.25e-08115
stem cell4.16e-0897
somatic cell4.72e-08118


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)
MA0003.10.261277
MA0004.10.330313
MA0006.10.186435
MA0007.10.850001
MA0009.10.743257
MA0014.10.144697
MA0017.10.598706
MA0019.11.39291
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.14.03288
MA0029.10.679737
MA0030.10.686088
MA0031.10.651724
MA0038.10.462726
MA0040.10.755433
MA0041.10.263922
MA0042.10.252679
MA0043.10.837621
MA0046.10.778239
MA0048.10.199479
MA0050.10.365212
MA0051.11.18756
MA0052.10.76328
MA0055.10.0098576
MA0056.10
MA0057.10.181039
MA0058.10.246908
MA0059.10.257372
MA0060.10.12537
MA0061.10.884293
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.11.12865
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.10.00168399
MA0074.10.419185
MA0076.13.43847
MA0077.10.724865
MA0078.10.502121
MA0081.10.760108
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.534411
MA0089.10
MA0090.10.299987
MA0091.10.342071
MA0092.10.300264
MA0093.10.20148
MA0095.10
MA0098.10
MA0100.10.408523
MA0101.12.07249
MA0103.10.216742
MA0105.10.26272
MA0106.10.509454
MA0107.11.79018
MA0108.20.589413
MA0109.10
MA0111.11.51846
MA0113.10.482899
MA0114.10.876865
MA0115.10.84036
MA0116.10.546914
MA0117.10.808813
MA0119.10.265536
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.11.11539
MA0139.11.14144
MA0140.10.408417
MA0141.10.233109
MA0142.10.63775
MA0143.10.49828
MA0144.10.147954
MA0145.10.133285
MA0146.10.775515
MA0147.10.157258
MA0148.10.344843
MA0149.10.269772
MA0062.24.72866
MA0035.20.412747
MA0039.21.36945
MA0138.20.555696
MA0002.20.343346
MA0137.20.230686
MA0104.20.11535
MA0047.20.46201
MA0112.20.0329566
MA0065.20.314773
MA0150.10.316876
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.195907
MA0155.10.154271
MA0156.10.634231
MA0157.10.606944
MA0158.10
MA0159.10.495113
MA0160.10.347545
MA0161.10
MA0162.10.103104
MA0163.10.563751
MA0164.10.437937
MA0080.20.609443
MA0018.20.446948
MA0099.20.549696
MA0079.20.00532751
MA0102.21.45844
MA0258.10.135621
MA0259.10.455671
MA0442.10
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