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MCL coexpression mm9:1060: Difference between revisions

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{{MCL_coexpression_mm9
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plasma membrane;6.91408372259676e-06;16403,13405,192897!GO:0046847;filopodium formation;3.45685239974223e-05;16403,192897!GO:0030035;microspike biogenesis;3.45685239974223e-05;16403,192897!GO:0008305;integrin complex;0.000322932264887892;16403,192897!GO:0030031;cell projection biogenesis;0.000519188727130741;16403,192897!GO:0007160;cell-matrix adhesion;0.000726398330933817;16403,192897!GO:0031589;cell-substrate adhesion;0.000726398330933817;16403,192897!GO:0043235;receptor complex;0.000734641541604711;16403,192897!GO:0007229;integrin-mediated signaling pathway;0.00104547518096533;16403,192897!GO:0044459;plasma membrane part;0.00560911464321391;16403,13405,192897!GO:0043234;protein complex;0.00560911464321391;16403,13405,192897!GO:0032990;cell part morphogenesis;0.00560911464321391;16403,192897!GO:0030030;cell projection organization and biogenesis;0.00560911464321391;16403,192897!GO:0048858;cell projection morphogenesis;0.00560911464321391;16403,192897!GO:0022409;positive regulation of cell-cell adhesion;0.00560911464321391;16403!GO:0033627;cell adhesion mediated by integrin;0.00657282106793939;16403!GO:0045213;neurotransmitter receptor metabolic process;0.00742301469348088;13405!GO:0005886;plasma membrane;0.00763556598579442;16403,13405,192897!GO:0048856;anatomical structure development;0.00763556598579442;16403,13405,192897!GO:0032991;macromolecular complex;0.00788565669744276;16403,13405,192897!GO:0009925;basal plasma membrane;0.00788565669744276;192897!GO:0046716;muscle maintenance;0.00788565669744276;13405!GO:0045178;basal part of cell;0.00788565669744276;192897!GO:0022407;regulation of cell-cell adhesion;0.00788565669744276;16403!GO:0007275;multicellular organismal development;0.00813724320940646;16403,13405,192897!GO:0005626;insoluble fraction;0.00840998445350211;13405!GO:0000902;cell morphogenesis;0.00840998445350211;16403,192897!GO:0032989;cellular structure morphogenesis;0.00840998445350211;16403,192897!GO:0016010;dystrophin-associated glycoprotein complex;0.00840998445350211;13405!GO:0045785;positive regulation of cell adhesion;0.00840998445350211;16403!GO:0022610;biological adhesion;0.0121661972780957;16403,192897!GO:0007155;cell adhesion;0.0121661972780957;16403,192897!GO:0005178;integrin binding;0.013635432305403;16403!GO:0032502;developmental process;0.013635432305403;16403,13405,192897!GO:0043112;receptor metabolic process;0.0150071331185883;13405!GO:0005605;basal lamina;0.0151730473234393;13405!GO:0042383;sarcolemma;0.0158968347703766;13405!GO:0030018;Z disc;0.0164326859735878;13405!GO:0050900;leukocyte migration;0.0164326859735878;16403!GO:0005509;calcium ion binding;0.0164326859735878;16403,13405!GO:0031674;I band;0.0164326859735878;13405!GO:0045121;lipid raft;0.0164326859735878;13405!GO:0005887;integral to plasma membrane;0.0164326859735878;16403,192897!GO:0030055;cell-matrix junction;0.0164326859735878;13405!GO:0031226;intrinsic to plasma membrane;0.0164326859735878;16403,192897!GO:0042475;odontogenesis of dentine-containing teeth;0.0164326859735878;16403!GO:0042476;odontogenesis;0.0169746959812294;16403!GO:0030155;regulation of cell adhesion;0.019675277020939;16403!GO:0032403;protein complex binding;0.0209823593345206;16403!GO:0007154;cell communication;0.0219724178169959;16403,13405,192897!GO:0005604;basement membrane;0.0250256412289942;13405!GO:0032501;multicellular organismal process;0.0250256412289942;16403,13405,192897!GO:0009653;anatomical structure morphogenesis;0.0256212059399399;16403,192897!GO:0030017;sarcomere;0.0256212059399399;13405!GO:0044449;contractile fiber part;0.0262944639637175;13405!GO:0030016;myofibril;0.0280613268978502;13405!GO:0043292;contractile fiber;0.0283010912373617;13405!GO:0048513;organ development;0.0326411658096284;16403,13405!GO:0044420;extracellular matrix part;0.0326411658096284;13405!GO:0007519;skeletal muscle development;0.033138335906351;13405!GO:0005515;protein binding;0.0369853357259542;16403,13405,192897!GO:0014706;striated muscle development;0.0411228079628484;13405!GO:0009897;external side of plasma membrane;0.0450794982652343;16403!GO:0048731;system development;0.0451373732717434;16403,13405!GO:0005792;microsome;0.049108109726202;13405!GO:0042598;vesicular 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|gostat_on_MCL_coexpression=GO:0016323;basolateral plasma membrane;6.91408372259676e-06;16403,13405,192897!GO:0046847;filopodium formation;3.45685239974223e-05;16403,192897!GO:0030035;microspike biogenesis;3.45685239974223e-05;16403,192897!GO:0008305;integrin complex;0.000322932264887892;16403,192897!GO:0030031;cell projection biogenesis;0.000519188727130741;16403,192897!GO:0007160;cell-matrix adhesion;0.000726398330933817;16403,192897!GO:0031589;cell-substrate adhesion;0.000726398330933817;16403,192897!GO:0043235;receptor complex;0.000734641541604711;16403,192897!GO:0007229;integrin-mediated signaling pathway;0.00104547518096533;16403,192897!GO:0044459;plasma membrane part;0.00560911464321391;16403,13405,192897!GO:0043234;protein complex;0.00560911464321391;16403,13405,192897!GO:0032990;cell part morphogenesis;0.00560911464321391;16403,192897!GO:0030030;cell projection organization and biogenesis;0.00560911464321391;16403,192897!GO:0048858;cell projection morphogenesis;0.00560911464321391;16403,192897!GO:0022409;positive regulation of cell-cell adhesion;0.00560911464321391;16403!GO:0033627;cell adhesion mediated by integrin;0.00657282106793939;16403!GO:0045213;neurotransmitter receptor metabolic process;0.00742301469348088;13405!GO:0005886;plasma membrane;0.00763556598579442;16403,13405,192897!GO:0048856;anatomical structure development;0.00763556598579442;16403,13405,192897!GO:0032991;macromolecular complex;0.00788565669744276;16403,13405,192897!GO:0009925;basal plasma membrane;0.00788565669744276;192897!GO:0046716;muscle maintenance;0.00788565669744276;13405!GO:0045178;basal part of cell;0.00788565669744276;192897!GO:0022407;regulation of cell-cell adhesion;0.00788565669744276;16403!GO:0007275;multicellular organismal development;0.00813724320940646;16403,13405,192897!GO:0005626;insoluble fraction;0.00840998445350211;13405!GO:0000902;cell morphogenesis;0.00840998445350211;16403,192897!GO:0032989;cellular structure morphogenesis;0.00840998445350211;16403,192897!GO:0016010;dystrophin-associated glycoprotein complex;0.00840998445350211;13405!GO:0045785;positive regulation of cell adhesion;0.00840998445350211;16403!GO:0022610;biological adhesion;0.0121661972780957;16403,192897!GO:0007155;cell adhesion;0.0121661972780957;16403,192897!GO:0005178;integrin binding;0.013635432305403;16403!GO:0032502;developmental process;0.013635432305403;16403,13405,192897!GO:0043112;receptor metabolic process;0.0150071331185883;13405!GO:0005605;basal lamina;0.0151730473234393;13405!GO:0042383;sarcolemma;0.0158968347703766;13405!GO:0030018;Z disc;0.0164326859735878;13405!GO:0050900;leukocyte migration;0.0164326859735878;16403!GO:0005509;calcium ion binding;0.0164326859735878;16403,13405!GO:0031674;I band;0.0164326859735878;13405!GO:0045121;lipid raft;0.0164326859735878;13405!GO:0005887;integral to plasma membrane;0.0164326859735878;16403,192897!GO:0030055;cell-matrix junction;0.0164326859735878;13405!GO:0031226;intrinsic to plasma membrane;0.0164326859735878;16403,192897!GO:0042475;odontogenesis of dentine-containing teeth;0.0164326859735878;16403!GO:0042476;odontogenesis;0.0169746959812294;16403!GO:0030155;regulation of cell adhesion;0.019675277020939;16403!GO:0032403;protein complex binding;0.0209823593345206;16403!GO:0007154;cell communication;0.0219724178169959;16403,13405,192897!GO:0005604;basement membrane;0.0250256412289942;13405!GO:0032501;multicellular organismal process;0.0250256412289942;16403,13405,192897!GO:0009653;anatomical structure morphogenesis;0.0256212059399399;16403,192897!GO:0030017;sarcomere;0.0256212059399399;13405!GO:0044449;contractile fiber part;0.0262944639637175;13405!GO:0030016;myofibril;0.0280613268978502;13405!GO:0043292;contractile fiber;0.0283010912373617;13405!GO:0048513;organ development;0.0326411658096284;16403,13405!GO:0044420;extracellular matrix part;0.0326411658096284;13405!GO:0007519;skeletal muscle development;0.033138335906351;13405!GO:0005515;protein binding;0.0369853357259542;16403,13405,192897!GO:0014706;striated muscle development;0.0411228079628484;13405!GO:0009897;external side of plasma membrane;0.0450794982652343;16403!GO:0048731;system development;0.0451373732717434;16403,13405!GO:0005792;microsome;0.049108109726202;13405!GO:0042598;vesicular fraction;0.0496175611299744;13405!
}}

Latest revision as of 16:19, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:115836183..115836190,+p16@Itgb4
Mm9::chr1:159186758..159186781,-p5@Rasal2
Mm9::chr2:71625071..71625102,+p3@Itga6
Mm9::chr2:71625114..71625140,+p2@Itga6
Mm9::chr4:96214495..96214500,-p@chr4:96214495..96214500
-
Mm9::chrX:82018040..82018058,+p4@Dmd
Mm9::chrX:82018062..82018069,+p25@Dmd


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:0016323basolateral plasma membrane6.91408372259676e-06
GO:0046847filopodium formation3.45685239974223e-05
GO:0030035microspike biogenesis3.45685239974223e-05
GO:0008305integrin complex0.000322932264887892
GO:0030031cell projection biogenesis0.000519188727130741
GO:0007160cell-matrix adhesion0.000726398330933817
GO:0031589cell-substrate adhesion0.000726398330933817
GO:0043235receptor complex0.000734641541604711
GO:0007229integrin-mediated signaling pathway0.00104547518096533
GO:0044459plasma membrane part0.00560911464321391
GO:0043234protein complex0.00560911464321391
GO:0032990cell part morphogenesis0.00560911464321391
GO:0030030cell projection organization and biogenesis0.00560911464321391
GO:0048858cell projection morphogenesis0.00560911464321391
GO:0022409positive regulation of cell-cell adhesion0.00560911464321391
GO:0033627cell adhesion mediated by integrin0.00657282106793939
GO:0045213neurotransmitter receptor metabolic process0.00742301469348088
GO:0005886plasma membrane0.00763556598579442
GO:0048856anatomical structure development0.00763556598579442
GO:0032991macromolecular complex0.00788565669744276
GO:0009925basal plasma membrane0.00788565669744276
GO:0046716muscle maintenance0.00788565669744276
GO:0045178basal part of cell0.00788565669744276
GO:0022407regulation of cell-cell adhesion0.00788565669744276
GO:0007275multicellular organismal development0.00813724320940646
GO:0005626insoluble fraction0.00840998445350211
GO:0000902cell morphogenesis0.00840998445350211
GO:0032989cellular structure morphogenesis0.00840998445350211
GO:0016010dystrophin-associated glycoprotein complex0.00840998445350211
GO:0045785positive regulation of cell adhesion0.00840998445350211
GO:0022610biological adhesion0.0121661972780957
GO:0007155cell adhesion0.0121661972780957
GO:0005178integrin binding0.013635432305403
GO:0032502developmental process0.013635432305403
GO:0043112receptor metabolic process0.0150071331185883
GO:0005605basal lamina0.0151730473234393
GO:0042383sarcolemma0.0158968347703766
GO:0030018Z disc0.0164326859735878
GO:0050900leukocyte migration0.0164326859735878
GO:0005509calcium ion binding0.0164326859735878
GO:0031674I band0.0164326859735878
GO:0045121lipid raft0.0164326859735878
GO:0005887integral to plasma membrane0.0164326859735878
GO:0030055cell-matrix junction0.0164326859735878
GO:0031226intrinsic to plasma membrane0.0164326859735878
GO:0042475odontogenesis of dentine-containing teeth0.0164326859735878
GO:0042476odontogenesis0.0169746959812294
GO:0030155regulation of cell adhesion0.019675277020939
GO:0032403protein complex binding0.0209823593345206
GO:0007154cell communication0.0219724178169959
GO:0005604basement membrane0.0250256412289942
GO:0032501multicellular organismal process0.0250256412289942
GO:0009653anatomical structure morphogenesis0.0256212059399399
GO:0030017sarcomere0.0256212059399399
GO:0044449contractile fiber part0.0262944639637175
GO:0030016myofibril0.0280613268978502
GO:0043292contractile fiber0.0283010912373617
GO:0048513organ development0.0326411658096284
GO:0044420extracellular matrix part0.0326411658096284
GO:0007519skeletal muscle development0.033138335906351
GO:0005515protein binding0.0369853357259542
GO:0014706striated muscle development0.0411228079628484
GO:0009897external side of plasma membrane0.0450794982652343
GO:0048731system development0.0451373732717434
GO:0005792microsome0.049108109726202
GO:0042598vesicular fraction0.0496175611299744



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>

Cell Type
Ontology termp-valuen
autonomic neuron3.42e-129

Uber Anatomy
Ontology termp-valuen
peripheral nervous system5.47e-1511
autonomic nervous system3.42e-129


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)
MA0003.11.4232
MA0004.10.481116
MA0006.10.311391
MA0007.11.17655
MA0009.10.92425
MA0014.15.99891
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
MA0046.10.960497
MA0048.14.04772
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.362005
MA0056.10
MA0057.10.376102
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.385183
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.11.3018
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
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.11.62423
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
MA0144.12.05933
MA0145.10.631666
MA0146.11.57153
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.500692
MA0035.21.40435
MA0039.23.91294
MA0138.20.727395
MA0002.20.205289
MA0137.20.957645
MA0104.20.218974
MA0047.20.626803
MA0112.20.0910939
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.10.336768
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.302441
MA0163.10.519779
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.21.47363
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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