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MCL coexpression mm9:792: Difference between revisions

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{{MCL_coexpression_mm9
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complex;0.00580002165270492;232440,68089,14707,11974,66172!GO:0008154;actin polymerization and/or depolymerization;0.00602443029504808;68089,12631!GO:0032991;macromolecular complex;0.00602443029504808;232440,68089,14707,11974,66172!GO:0044446;intracellular organelle part;0.00776976149973157;232440,68089,12631,11974,66172!GO:0044422;organelle part;0.00776976149973157;232440,68089,12631,11974,66172!GO:0030836;positive regulation of actin filament depolymerization;0.0253074409282662;12631!GO:0001842;neural fold formation;0.0299583719443181;12631!GO:0030036;actin cytoskeleton organization and biogenesis;0.0299583719443181;68089,12631!GO:0030029;actin filament-based process;0.0305337940963763;68089,12631!GO:0015629;actin cytoskeleton;0.036334407086668;68089,12631!GO:0051130;positive regulation of cellular component organization and biogenesis;0.0404586405716512;12631!GO:0015991;ATP hydrolysis coupled proton transport;0.0404586405716512;11974!GO:0005885;Arp2/3 protein complex;0.0404586405716512;68089!GO:0003779;actin binding;0.0404586405716512;68089,12631!GO:0015988;energy coupled proton transport, against electrochemical 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|gostat_on_MCL_coexpression=GO:0043234;protein complex;0.00580002165270492;232440,68089,14707,11974,66172!GO:0008154;actin polymerization and/or depolymerization;0.00602443029504808;68089,12631!GO:0032991;macromolecular complex;0.00602443029504808;232440,68089,14707,11974,66172!GO:0044446;intracellular organelle part;0.00776976149973157;232440,68089,12631,11974,66172!GO:0044422;organelle part;0.00776976149973157;232440,68089,12631,11974,66172!GO:0030836;positive regulation of actin filament depolymerization;0.0253074409282662;12631!GO:0001842;neural fold formation;0.0299583719443181;12631!GO:0030036;actin cytoskeleton organization and biogenesis;0.0299583719443181;68089,12631!GO:0030029;actin filament-based process;0.0305337940963763;68089,12631!GO:0015629;actin cytoskeleton;0.036334407086668;68089,12631!GO:0051130;positive regulation of cellular component organization and biogenesis;0.0404586405716512;12631!GO:0015991;ATP hydrolysis coupled proton transport;0.0404586405716512;11974!GO:0005885;Arp2/3 protein complex;0.0404586405716512;68089!GO:0003779;actin binding;0.0404586405716512;68089,12631!GO:0015988;energy coupled proton transport, against electrochemical gradient;0.0404586405716512;11974!
|ontology_enrichment_celltype=CL:0000219!3.23e-15!54;CL:0002320!4.62e-11!46;CL:0000134!4.62e-11!46;CL:0002371!8.07e-11!118;CL:0000548!1.83e-09!115;CL:0000255!1.83e-09!115;CL:0000988!2.64e-07!32;CL:0002032!2.64e-07!32;CL:0000037!2.64e-07!32;CL:0000566!2.64e-07!32;CL:0000837!2.64e-07!32;CL:0000333!5.97e-07!10;CL:0000095!5.97e-07!10;CL:0000243!5.97e-07!10;CL:0000123!5.97e-07!10;CL:0000125!5.97e-07!10;CL:0000030!5.97e-07!10;CL:0000339!5.97e-07!10
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!4.62e-11!46;UBERON:0002204!3.64e-09!32;UBERON:0002371!4.38e-08!16
|tfbs_overrepresentation_for_novel_motifs=0.93395,0.433653,0.879518,0.394491,0.227651,1.05171,0.495658,2.03865,0.154135,0.0330111,0.453212,0.484001,0.449446,0.507558,0.24249,0,0.696644,0.22065,0.134657,0.0703872,0.296085,0.179861,1.26371,0.64218,0.337218,0.534339,0.128175,0.428336,0.268347,0.319094,0.414842,0.796599,0.624261,0.735537,0.242923,0.00999634,1.78391,1.20775,0.559915,0.167387,0.224094,0.419787,0.371854,0.244285,0.812975,0.998423,1.49936,0.443479,0.314152,1.36808,0.679429,0.560572,0.30602,0.937018,0.954342,1.28038,1.39791,0.471658,0.384731,0.512521,0.776777,0.569793,0.492158,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.151245,0.424998,0.987652,1.22652,0.107966,0.113315,0.607043,0.759798,0.299972,0.152219,0.713779,0.568383,0.14134,0.873141,0.967095,0.439624,0.0965007,0.623015,1.60001,1.15927,0.878077,1.89585,0.657661,0.188213,0.17334,0.14449,0.812053,0.618454,0.0816605,0.210602,0.796322,0.919715,0.680015,0.678976,1.07585,0.737915,0.439611,1.48974,0.297733,0.348012,0.921485,0.301014,0.458194,1.16629,0.222515,0.496288,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,1.00644,1.05894,0.527782,1.18781,0.177062,0.951467,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.229209,0.665499,0.369078,0.938577,0.178329,0.526881,1.01974,0.561556,0.253271,0.352329,0.950885,1.1483,0.872292,0.763895,0.914544,0.669337,0.519673,0.602679,0.482466,0.254444
|tfbs_overrepresentation_jaspar=MA0003.1;0.458525,MA0004.1;1.02263,MA0006.1;0.238555,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;0.433479,MA0017.1;0.726051,MA0019.1;1.551,MA0024.1;0.779446,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;2.77501,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;0.729293,MA0038.1;0.534262,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.589612,MA0050.1;0.431976,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.692644,MA0056.1;0,MA0057.1;0.258928,MA0058.1;2.27565,MA0059.1;0.316585,MA0060.1;0.9744,MA0061.1;0.56663,MA0063.1;0,MA0066.1;0.523573,MA0067.1;2.62093,MA0068.1;0.563625,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;0.000250057,MA0074.1;0.488775,MA0076.1;2.9863,MA0077.1;0.804033,MA0078.1;0.575205,MA0081.1;0.338098,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;0.413524,MA0089.1;0,MA0090.1;0.362551,MA0091.1;0.407455,MA0092.1;0.362847,MA0093.1;1.30984,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;0.324888,MA0103.1;0.272167,MA0105.1;0.35523,MA0106.1;1.42499,MA0107.1;0.73569,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;0.555251,MA0114.1;1.06861,MA0115.1;0.921497,MA0116.1;0.238371,MA0117.1;0.88947,MA0119.1;0.325434,MA0122.1;0.909168,MA0124.1;1.11203,MA0125.1;1.03833,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.143341,MA0140.1;0.477483,MA0141.1;0.29014,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;0.200183,MA0146.1;0.77944,MA0147.1;0.205697,MA0148.1;0.410398,MA0149.1;0.330018,MA0062.2;6.35383,MA0035.2;0.482026,MA0039.2;2.7644,MA0138.2;0.630612,MA0002.2;0.877049,MA0137.2;0.783415,MA0104.2;0.476119,MA0047.2;1.32079,MA0112.2;0.200175,MA0065.2;0.0545595,MA0150.1;0.380623,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.581988,MA0155.1;0.490492,MA0156.1;1.39718,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.214506,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.348617,MA0163.1;0.0600297,MA0164.1;0.508398,MA0080.2;0.267388,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;0.968591,MA0102.2;1.5442,MA0258.1;0.180934,MA0259.1;0.196451,MA0442.1;0
}}

Latest revision as of 15:53, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:70265407..70265452,+p1@Med11
Mm9::chr17:26813332..26813333,+p3@Atp6v0e
Mm9::chr17:26813335..26813346,+p2@Atp6v0e
Mm9::chr17:26813350..26813411,+p1@Atp6v0e
Mm9::chr19:5490512..5490525,+p1@Cfl1
p1@LOC100048522
Mm9::chr3:146162814..146162850,+p1@Gm13342
p1@Gm15776
p1@Gm4356
p1@Gng5
p1@LOC100048410
Mm9::chr5:124928339..124928393,-p1@Rilpl2
Mm9::chr6:113328152..113328185,+p1@Arpc4
Mm9::chr6:136756784..136756866,+p1@H2afj


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:0043234protein complex0.00580002165270492
GO:0008154actin polymerization and/or depolymerization0.00602443029504808
GO:0032991macromolecular complex0.00602443029504808
GO:0044446intracellular organelle part0.00776976149973157
GO:0044422organelle part0.00776976149973157
GO:0030836positive regulation of actin filament depolymerization0.0253074409282662
GO:0001842neural fold formation0.0299583719443181
GO:0030036actin cytoskeleton organization and biogenesis0.0299583719443181
GO:0030029actin filament-based process0.0305337940963763
GO:0015629actin cytoskeleton0.036334407086668
GO:0051130positive regulation of cellular component organization and biogenesis0.0404586405716512
GO:0015991ATP hydrolysis coupled proton transport0.0404586405716512
GO:0005885Arp2/3 protein complex0.0404586405716512
GO:0003779actin binding0.0404586405716512
GO:0015988energy coupled proton transport, against electrochemical gradient0.0404586405716512



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
connective tissue4.62e-1146
musculoskeletal system3.64e-0932
bone marrow4.38e-0816


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)
MA0003.10.458525
MA0004.11.02263
MA0006.10.238555
MA0007.10.38073
MA0009.10.82278
MA0014.10.433479
MA0017.10.726051
MA0019.11.551
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.12.77501
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
MA0048.10.589612
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.692644
MA0056.10
MA0057.10.258928
MA0058.12.27565
MA0059.10.316585
MA0060.10.9744
MA0061.10.56663
MA0063.10
MA0066.10.523573
MA0067.12.62093
MA0068.10.563625
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.000250057
MA0074.10.488775
MA0076.12.9863
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.413524
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.11.30984
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.272167
MA0105.10.35523
MA0106.11.42499
MA0107.10.73569
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.11.06861
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
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
MA0144.10.195095
MA0145.10.200183
MA0146.10.77944
MA0147.10.205697
MA0148.10.410398
MA0149.10.330018
MA0062.26.35383
MA0035.20.482026
MA0039.22.7644
MA0138.20.630612
MA0002.20.877049
MA0137.20.783415
MA0104.20.476119
MA0047.21.32079
MA0112.20.200175
MA0065.20.0545595
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.581988
MA0155.10.490492
MA0156.11.39718
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.348617
MA0163.10.0600297
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.20.968591
MA0102.21.5442
MA0258.10.180934
MA0259.10.196451
MA0442.10
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