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MCL coexpression mm9:1105: Difference between revisions

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{{MCL_coexpression_mm9
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during inflammatory response;0.00690297485344875;12505!GO:0005540;hyaluronic acid binding;0.0344354514796465;12505!GO:0001658;ureteric bud branching;0.0344354514796465;12505!GO:0001657;ureteric bud development;0.0344354514796465;12505!GO:0001656;metanephros development;0.0344354514796465;12505!GO:0005089;Rho guanyl-nucleotide exchange factor activity;0.0344354514796465;263406!GO:0035023;regulation of Rho protein signal transduction;0.0344354514796465;263406!GO:0048754;branching morphogenesis of a tube;0.0344354514796465;12505!GO:0005088;Ras guanyl-nucleotide exchange factor activity;0.0344354514796465;263406!GO:0001763;morphogenesis of a branching structure;0.0344354514796465;12505!GO:0001822;kidney development;0.0344354514796465;12505!GO:0005539;glycosaminoglycan binding;0.0344354514796465;12505!GO:0001655;urogenital system development;0.0344354514796465;12505!GO:0042060;wound healing;0.0344354514796465;12505!GO:0007266;Rho protein signal transduction;0.0344354514796465;263406!GO:0030247;polysaccharide binding;0.0344354514796465;12505!GO:0001871;pattern binding;0.0344354514796465;12505!GO:0046578;regulation of Ras protein signal transduction;0.0382458542655602;263406!GO:0005085;guanyl-nucleotide exchange factor activity;0.0429970388807503;263406!GO:0051056;regulation of small GTPase mediated signal transduction;0.0429970388807503;263406!GO:0009897;external side of plasma membrane;0.043252751891532;12505!GO:0035239;tube morphogenesis;0.043252751891532;12505!GO:0007265;Ras protein signal transduction;0.043252751891532;263406!GO:0005083;small GTPase regulator 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|gostat_on_MCL_coexpression=GO:0002246;healing during inflammatory response;0.00690297485344875;12505!GO:0005540;hyaluronic acid binding;0.0344354514796465;12505!GO:0001658;ureteric bud branching;0.0344354514796465;12505!GO:0001657;ureteric bud development;0.0344354514796465;12505!GO:0001656;metanephros development;0.0344354514796465;12505!GO:0005089;Rho guanyl-nucleotide exchange factor activity;0.0344354514796465;263406!GO:0035023;regulation of Rho protein signal transduction;0.0344354514796465;263406!GO:0048754;branching morphogenesis of a tube;0.0344354514796465;12505!GO:0005088;Ras guanyl-nucleotide exchange factor activity;0.0344354514796465;263406!GO:0001763;morphogenesis of a branching structure;0.0344354514796465;12505!GO:0001822;kidney development;0.0344354514796465;12505!GO:0005539;glycosaminoglycan binding;0.0344354514796465;12505!GO:0001655;urogenital system development;0.0344354514796465;12505!GO:0042060;wound healing;0.0344354514796465;12505!GO:0007266;Rho protein signal transduction;0.0344354514796465;263406!GO:0030247;polysaccharide binding;0.0344354514796465;12505!GO:0001871;pattern binding;0.0344354514796465;12505!GO:0046578;regulation of Ras protein signal transduction;0.0382458542655602;263406!GO:0005085;guanyl-nucleotide exchange factor activity;0.0429970388807503;263406!GO:0051056;regulation of small GTPase mediated signal transduction;0.0429970388807503;263406!GO:0009897;external side of plasma membrane;0.043252751891532;12505!GO:0035239;tube morphogenesis;0.043252751891532;12505!GO:0007265;Ras protein signal transduction;0.043252751891532;263406!GO:0005083;small GTPase regulator activity;0.043252751891532;263406!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002204!1.95e-10!32;UBERON:0001474!4.74e-07!22;UBERON:0004765!4.74e-07!22;UBERON:0001434!4.74e-07!22;UBERON:0002371!6.03e-07!16
}}

Latest revision as of 16:24, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:77634618..77634633,+p2@Plekhg3
Mm9::chr2:102651988..102652001,-p@chr2:102651988..102652001
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Mm9::chr2:102653728..102653742,-p@chr2:102653728..102653742
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Mm9::chr2:102654028..102654039,-p@chr2:102654028..102654039
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Mm9::chr2:102654078..102654085,-p@chr2:102654078..102654085
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Mm9::chr2:102701761..102701783,-p@chr2:102701761..102701783
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Mm9::chr2:102741606..102741622,-p1@Cd44


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:0002246healing during inflammatory response0.00690297485344875
GO:0005540hyaluronic acid binding0.0344354514796465
GO:0001658ureteric bud branching0.0344354514796465
GO:0001657ureteric bud development0.0344354514796465
GO:0001656metanephros development0.0344354514796465
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0344354514796465
GO:0035023regulation of Rho protein signal transduction0.0344354514796465
GO:0048754branching morphogenesis of a tube0.0344354514796465
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0344354514796465
GO:0001763morphogenesis of a branching structure0.0344354514796465
GO:0001822kidney development0.0344354514796465
GO:0005539glycosaminoglycan binding0.0344354514796465
GO:0001655urogenital system development0.0344354514796465
GO:0042060wound healing0.0344354514796465
GO:0007266Rho protein signal transduction0.0344354514796465
GO:0030247polysaccharide binding0.0344354514796465
GO:0001871pattern binding0.0344354514796465
GO:0046578regulation of Ras protein signal transduction0.0382458542655602
GO:0005085guanyl-nucleotide exchange factor activity0.0429970388807503
GO:0051056regulation of small GTPase mediated signal transduction0.0429970388807503
GO:0009897external side of plasma membrane0.043252751891532
GO:0035239tube morphogenesis0.043252751891532
GO:0007265Ras protein signal transduction0.043252751891532
GO:0005083small GTPase regulator activity0.043252751891532



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>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
musculoskeletal system1.95e-1032
bone element4.74e-0722
skeletal element4.74e-0722
skeletal system4.74e-0722
bone marrow6.03e-0716


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)
MA0003.10.188259
MA0004.10.481116
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.10.0886247
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.12.20556
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.0406078
MA0056.10
MA0057.10.117936
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.11.83304
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.152496
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.598004
MA0089.10
MA0090.11.98258
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.9471
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.0910975
MA0146.10.108739
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.014361
MA0138.20.727395
MA0002.20.592533
MA0137.20.365364
MA0104.20.624968
MA0047.20.626803
MA0112.20.0910939
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.11.5176
MA0153.11.07519
MA0154.10.126143
MA0155.10.336768
MA0156.10.936991
MA0157.10.781683
MA0158.10
MA0159.10.776527
MA0160.10.50056
MA0161.10
MA0162.10.127623
MA0163.12.64114
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.233827
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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