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MCL coexpression mm9:809: Difference between revisions

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{{MCL_coexpression_mm9
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complex;0.000977227371540093;68611,20090,66448,68565!GO:0003735;structural constituent of ribosome;0.000977227371540093;20090,66448,68565!GO:0005840;ribosome;0.000977227371540093;20090,66448,68565!GO:0005739;mitochondrion;0.00511310553386146;68611,66169,66448,68565!GO:0033279;ribosomal subunit;0.00511310553386146;20090,66448!GO:0032991;macromolecular complex;0.00511310553386146;68611,20022,20090,66448,68565!GO:0006412;translation;0.00723930261923568;20090,66448,68565!GO:0005666;DNA-directed RNA polymerase III complex;0.0117906437470871;20022!GO:0009059;macromolecule biosynthetic process;0.0184646870897222;20090,66448,68565!GO:0044444;cytoplasmic part;0.02519769300812;68611,20090,66169,66448,68565!GO:0044249;cellular biosynthetic process;0.033176034383354;20090,66448,68565!GO:0000428;DNA-directed RNA polymerase complex;0.0357435504572228;20022!GO:0055029;nuclear DNA-directed RNA polymerase complex;0.0357435504572228;20022!GO:0015450;P-P-bond-hydrolysis-driven protein transmembrane transporter activity;0.0357435504572228;66169!GO:0022884;macromolecule transmembrane transporter activity;0.0357435504572228;66169!GO:0030880;RNA polymerase complex;0.0357435504572228;20022!GO:0005843;cytosolic small ribosomal subunit (sensu Eukaryota);0.0357435504572228;20090!GO:0044429;mitochondrial part;0.0357435504572228;66169,66448!GO:0044446;intracellular organelle part;0.0357435504572228;20022,20090,66169,66448!GO:0044422;organelle part;0.0357435504572228;20022,20090,66169,66448!GO:0000315;organellar large ribosomal subunit;0.0357435504572228;66448!GO:0005762;mitochondrial large ribosomal subunit;0.0357435504572228;66448!GO:0009058;biosynthetic process;0.0357435504572228;20090,66448,68565!GO:0005741;mitochondrial outer membrane;0.0357435504572228;66169!GO:0008320;protein transmembrane transporter activity;0.0357435504572228;66169!GO:0031968;organelle outer membrane;0.0397758379675364;66169!GO:0019843;rRNA binding;0.0400371094597319;66448!GO:0010467;gene 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|gostat_on_MCL_coexpression=GO:0030529;ribonucleoprotein complex;0.000977227371540093;68611,20090,66448,68565!GO:0003735;structural constituent of ribosome;0.000977227371540093;20090,66448,68565!GO:0005840;ribosome;0.000977227371540093;20090,66448,68565!GO:0005739;mitochondrion;0.00511310553386146;68611,66169,66448,68565!GO:0033279;ribosomal subunit;0.00511310553386146;20090,66448!GO:0032991;macromolecular complex;0.00511310553386146;68611,20022,20090,66448,68565!GO:0006412;translation;0.00723930261923568;20090,66448,68565!GO:0005666;DNA-directed RNA polymerase III complex;0.0117906437470871;20022!GO:0009059;macromolecule biosynthetic process;0.0184646870897222;20090,66448,68565!GO:0044444;cytoplasmic part;0.02519769300812;68611,20090,66169,66448,68565!GO:0044249;cellular biosynthetic process;0.033176034383354;20090,66448,68565!GO:0000428;DNA-directed RNA polymerase complex;0.0357435504572228;20022!GO:0055029;nuclear DNA-directed RNA polymerase complex;0.0357435504572228;20022!GO:0015450;P-P-bond-hydrolysis-driven protein transmembrane transporter activity;0.0357435504572228;66169!GO:0022884;macromolecule transmembrane transporter activity;0.0357435504572228;66169!GO:0030880;RNA polymerase complex;0.0357435504572228;20022!GO:0005843;cytosolic small ribosomal subunit (sensu Eukaryota);0.0357435504572228;20090!GO:0044429;mitochondrial part;0.0357435504572228;66169,66448!GO:0044446;intracellular organelle part;0.0357435504572228;20022,20090,66169,66448!GO:0044422;organelle part;0.0357435504572228;20022,20090,66169,66448!GO:0000315;organellar large ribosomal subunit;0.0357435504572228;66448!GO:0005762;mitochondrial large ribosomal subunit;0.0357435504572228;66448!GO:0009058;biosynthetic process;0.0357435504572228;20090,66448,68565!GO:0005741;mitochondrial outer membrane;0.0357435504572228;66169!GO:0008320;protein transmembrane transporter activity;0.0357435504572228;66169!GO:0031968;organelle outer membrane;0.0397758379675364;66169!GO:0019843;rRNA binding;0.0400371094597319;66448!GO:0010467;gene expression;0.0473908350928618;20022,20090,66448,68565!GO:0015935;small ribosomal subunit;0.0485648897514198;20090!
|ontology_enrichment_celltype=CL:0000548!1.67e-23!115;CL:0000255!1.67e-23!115;CL:0002371!7.84e-23!118;CL:0000723!1.09e-19!91;CL:0000048!1.09e-19!91;CL:0000034!1.58e-18!97;CL:0000055!8.49e-17!49;CL:0002319!1.21e-15!43;CL:0000221!1.23e-15!44;CL:0000133!1.23e-15!44;CL:0002321!3.67e-15!70;CL:0000393!6.62e-12!39;CL:0000211!6.62e-12!39;CL:0000117!3.55e-11!23;CL:0000337!3.55e-11!23;CL:0000540!8.38e-11!33;CL:0000047!8.38e-11!33;CL:0000031!8.38e-11!33;CL:0000404!8.38e-11!33;CL:0000219!3.08e-10!54;CL:0002320!3.24e-07!46;CL:0000134!3.24e-07!46
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!1.42e-10!75;UBERON:0001017!2.20e-10!73;UBERON:0002020!6.87e-10!34;UBERON:0003528!8.39e-08!29;UBERON:0002791!8.39e-08!29;UBERON:0001893!8.39e-08!29;UBERON:0000073!1.66e-07!54;UBERON:0002384!3.24e-07!46
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.433653,0.330161,0.394491,0.227651,0.40827,0.495658,0.448965,0.468136,0.133458,0.453212,1.21524,0.449446,0.507558,0.680035,0,1.66303,0.62892,0.134657,0.528436,0.296085,0.179861,1.26371,0.226287,0.895255,0.534339,0.402559,0.428336,0.268347,0.656973,1.06602,0.796599,0.624261,0.113369,0.242923,0.0500417,1.1396,0.480503,0.559915,0.167387,0.224094,0.419787,0.0422275,0.244285,0.317317,0.998423,1.49936,0.443479,0.314152,1.36808,0.679429,1.37808,0.633942,0.937018,0.954342,0.514504,0.279148,0.471658,0.384731,1.27615,0.776777,0.569793,0.952934,0.668331,0.525334,1.68713,1.08987,1.43807,1.81937,1.29123,0.31262,0.460931,0.745723,0.987652,0.748687,0.710896,0.364033,0.607043,0.759798,0.299972,0.463363,0.713779,0.568383,0.436063,0.873141,0.395495,0.092683,0.0965007,1.50944,1.60001,1.15927,0.878077,0.809272,0.657661,0.551605,0.17334,0.14449,0.812053,0.618454,0.987389,0.605162,0.796322,0.919715,0.680015,0.678976,1.89067,0.737915,0.439611,0.30446,0.806647,0.348012,0.921485,0.301014,0.458194,1.16629,0.222515,0.496288,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,1.23559,0.90286,0.387557,1.05894,0.527782,1.18781,0.0467191,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,1.35119,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.649035,1.10522,0.369078,0.938577,0.178329,0.526881,1.01974,0.561556,0.253271,0.352329,0.950885,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,0.482466,0.12239
}}

Latest revision as of 15:55, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:70260096..70260120,-p1@Gm10059
p1@Gm14303
p1@Gm2581
p1@Rps29
Mm9::chr17:26260459..26260499,+p1@Mrpl28
Mm9::chr17:46247931..46247971,+p1@Mrps18a
Mm9::chr19:10278691..10278727,+p1@1810006K21Rik
Mm9::chr3:96001503..96001557,-p1@Bola1
Mm9::chr4:155177709..155177749,+p1@Mrpl20
Mm9::chr5:136592548..136592610,+p1@Polr2j
Mm9::chr5:23349903..23349969,-p1@Tomm7
Mm9::chr9:61762345..61762381,-p1@Gm11942
p1@Gm13777
p1@Rplp1


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:0030529ribonucleoprotein complex0.000977227371540093
GO:0003735structural constituent of ribosome0.000977227371540093
GO:0005840ribosome0.000977227371540093
GO:0005739mitochondrion0.00511310553386146
GO:0033279ribosomal subunit0.00511310553386146
GO:0032991macromolecular complex0.00511310553386146
GO:0006412translation0.00723930261923568
GO:0005666DNA-directed RNA polymerase III complex0.0117906437470871
GO:0009059macromolecule biosynthetic process0.0184646870897222
GO:0044444cytoplasmic part0.02519769300812
GO:0044249cellular biosynthetic process0.033176034383354
GO:0000428DNA-directed RNA polymerase complex0.0357435504572228
GO:0055029nuclear DNA-directed RNA polymerase complex0.0357435504572228
GO:0015450P-P-bond-hydrolysis-driven protein transmembrane transporter activity0.0357435504572228
GO:0022884macromolecule transmembrane transporter activity0.0357435504572228
GO:0030880RNA polymerase complex0.0357435504572228
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.0357435504572228
GO:0044429mitochondrial part0.0357435504572228
GO:0044446intracellular organelle part0.0357435504572228
GO:0044422organelle part0.0357435504572228
GO:0000315organellar large ribosomal subunit0.0357435504572228
GO:0005762mitochondrial large ribosomal subunit0.0357435504572228
GO:0009058biosynthetic process0.0357435504572228
GO:0005741mitochondrial outer membrane0.0357435504572228
GO:0008320protein transmembrane transporter activity0.0357435504572228
GO:0031968organelle outer membrane0.0397758379675364
GO:0019843rRNA binding0.0400371094597319
GO:0010467gene expression0.0473908350928618
GO:0015935small ribosomal subunit0.0485648897514198



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>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
nervous system1.42e-1075
central nervous system2.20e-1073
gray matter6.87e-1034
brain grey matter8.39e-0829
regional part of telencephalon8.39e-0829
telencephalon8.39e-0829
regional part of nervous system1.66e-0754
connective tissue3.24e-0746


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)
MA0003.10.0854318
MA0004.11.02263
MA0006.11.24699
MA0007.10.38073
MA0009.10.82278
MA0014.10.119217
MA0017.10.726051
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.13.64201
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.11.47862
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.424109
MA0056.10
MA0057.10.258928
MA0058.10.823526
MA0059.10.849123
MA0060.10.9744
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.266547
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.13.85717e-05
MA0074.10.488775
MA0076.13.90074
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.11.11906
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.95209
MA0093.11.30984
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.748482
MA0105.10.35523
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.561811
MA0115.10.921497
MA0116.11.24629
MA0117.10.88947
MA0119.10.868953
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.11.54167
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.143341
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.11.07908
MA0145.10.442138
MA0146.10.148686
MA0147.12.48306
MA0148.10.410398
MA0149.10.330018
MA0062.24.63303
MA0035.20.482026
MA0039.20.0156581
MA0138.20.630612
MA0002.20.447007
MA0137.21.42833
MA0104.21.48162
MA0047.20.533516
MA0112.20.200175
MA0065.20.0545595
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.276788
MA0155.10.0631765
MA0156.10.763978
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.0672805
MA0163.10.0600297
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.20.00199657
MA0102.21.5442
MA0258.10.180934
MA0259.11.08444
MA0442.10
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