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MCL coexpression mm9:878: Difference between revisions

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{{MCL_coexpression_mm9
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decarboxylase inhibitor activity;0.016159955885354;18245!GO:0042979;ornithine decarboxylase regulator activity;0.016159955885354;18245!GO:0006595;polyamine metabolic process;0.02584813721866;18245!GO:0000184;mRNA catabolic process, nonsense-mediated decay;0.02584813721866;60365!GO:0006402;mRNA catabolic process;0.0273101551622031;60365!GO:0003729;mRNA binding;0.0273101551622031;60365!GO:0006401;RNA catabolic process;0.0273101551622031;60365!GO:0051028;mRNA transport;0.0273101551622031;60365!GO:0050658;RNA transport;0.0273101551622031;60365!GO:0051236;establishment of RNA localization;0.0273101551622031;60365!GO:0050657;nucleic acid transport;0.0273101551622031;60365!GO:0006403;RNA localization;0.0273101551622031;60365!GO:0015931;nucleobase, nucleoside, nucleotide and nucleic acid transport;0.0273101551622031;60365!GO:0006576;biogenic amine metabolic process;0.0331823158039291;18245!GO:0006575;amino acid derivative metabolic 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|coexpression_dpi_cluster_scores_median=0.255452033203475,0.065002016191076,0.221947893822551,0.474545704103412,0.471514994570017,0.223110820673195,0.670772619004246,0.59189544625387,0.857279307871169,0.820425308036525,0.908309977122622,0.728048755807444,0.756014422271463,0.651777796085717,0,0.720323114459876,0.911694818462073,0.654959171886873,0.7468536150561,0.748527343733595,0,0,0.94469926280088,0.631882984969235,0.65843113657743,0.2645983963912,0.155567395918081,0.269952836963617,0.544407155132256,0.177265236423641,0.321590636619315,0.572660793269736,0,0,0.293086190057046,0.300466757177931,0.0806875710728457,0.075919512117871,0.329719243347044,0.091424613524979,0.441647142913664,0.429104149209262,0.281098971197596,0,0,0,0,0,0,0,0,0,0.914589173198647,0.946932654425158,0.947357486378366,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.688361898921099,0.509086868372733,0.712003146028013,0.639243382371494,0,0,0,0,0,0.034172782309542,0.511324265408794,0.807168834291913,0.246010516510563,0.828932918319508,0.66752122443244,1.18245271753561,0.784373120867564,0.865340706471885,0.848077447032495,0,0,0,0.0613961096489926,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.291114024213495,0.502543502074069,0.328076468853684,0,0,0.0514050548005424,0,0,0,0,0,0,0,0,0.0531247310291112,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.436651175857108,0.508530750134945,0,0,0.0875701595484165,0,0,0,0,0,0,0.0239809638088447,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0412915344116851,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0114726486541832,0,0,0,0,0.05268038312984,0,0,0,0,0,0,0,0.0753613107413788,0,0,0,0,0,0,0,0,0,0,0,0,0.872145067056024,0.745363539086934,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0407493349282708,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0330027737817202,0,0,0,0,0,0,0.027821827298607,0,0.267146409463255,0.310555455666037,0.26101810026711,0,0,0,0.00236356296788431,0,0,0,0,0,0.00645689049860515,0,0,0,0,0,0,0.0338991055318041,0,0.000267070622348986,0.0216534965544966,0,0,0,0,0,0,0,0,0,0,0,0.00409549081017577,0,0.0201939307380272,0,0,0,0.811437914187353,0.766546193045516,0.806304702841468,0,0.00236537792693123,0,0,0,0,0,0,0.420154283585504,0.0259633538483016,0,0,0,0,0,0,0,0,0,0,0.0513676113575023,0,0,0,0,0,0,0,0,0.0121269368029194,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0008073;ornithine decarboxylase inhibitor activity;0.016159955885354;18245!GO:0042979;ornithine decarboxylase regulator activity;0.016159955885354;18245!GO:0006595;polyamine metabolic process;0.02584813721866;18245!GO:0000184;mRNA catabolic process, nonsense-mediated decay;0.02584813721866;60365!GO:0006402;mRNA catabolic process;0.0273101551622031;60365!GO:0003729;mRNA binding;0.0273101551622031;60365!GO:0006401;RNA catabolic process;0.0273101551622031;60365!GO:0051028;mRNA transport;0.0273101551622031;60365!GO:0050658;RNA transport;0.0273101551622031;60365!GO:0051236;establishment of RNA localization;0.0273101551622031;60365!GO:0050657;nucleic acid transport;0.0273101551622031;60365!GO:0006403;RNA localization;0.0273101551622031;60365!GO:0015931;nucleobase, nucleoside, nucleotide and nucleic acid transport;0.0273101551622031;60365!GO:0006576;biogenic amine metabolic process;0.0331823158039291;18245!GO:0006575;amino acid derivative metabolic process;0.0374068710784698;18245!
|ontology_enrichment_celltype=CL:0002371!1.09e-17!118;CL:0000988!4.92e-17!32;CL:0002032!4.92e-17!32;CL:0000037!4.92e-17!32;CL:0000566!4.92e-17!32;CL:0000837!4.92e-17!32;CL:0000548!5.79e-16!115;CL:0000255!5.79e-16!115;CL:0002320!3.95e-15!46;CL:0000134!3.95e-15!46;CL:0002031!7.93e-15!25;CL:0000066!3.13e-14!25;CL:0002076!4.27e-14!15;CL:0000219!1.04e-13!54;CL:0000838!4.62e-12!12;CL:0000791!4.22e-11!9;CL:0000789!4.22e-11!9;CL:0002420!4.22e-11!9;CL:0002419!4.22e-11!9;CL:0000790!4.22e-11!9;CL:0000223!4.99e-11!20;CL:0000738!6.64e-11!17;CL:0002087!6.64e-11!17;CL:0000084!6.91e-11!11;CL:0000827!6.91e-11!11;CL:0000542!7.56e-11!13;CL:0000051!7.56e-11!13;CL:0000624!7.05e-10!8;CL:0000034!8.15e-10!97;CL:0002242!9.68e-10!16;CL:0000049!7.71e-08!19;CL:0000893!8.09e-08!6;CL:0002489!8.09e-08!6;CL:0000898!8.09e-08!6;CL:0000809!8.09e-08!6;CL:0000810!8.09e-08!6;CL:0000895!8.09e-08!6;CL:0000808!8.09e-08!6;CL:0000894!8.09e-08!6;CL:0000806!8.09e-08!6;CL:0000807!8.09e-08!6;CL:0000805!8.09e-08!6;CL:0002425!8.09e-08!6;CL:0002436!8.09e-08!6;CL:0002427!8.09e-08!6;CL:0002428!8.09e-08!6;CL:0002429!8.09e-08!6;CL:0002433!8.09e-08!6;CL:0002431!8.09e-08!6;CL:0002432!8.09e-08!6;CL:0002563!1.24e-07!9;CL:0002251!1.24e-07!9;CL:0000723!8.18e-07!91;CL:0000048!8.18e-07!91
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!3.95e-15!46;UBERON:0000344!1.60e-10!15;UBERON:0000485!7.17e-09!11;UBERON:0001242!8.86e-09!13;UBERON:0000060!8.86e-09!13;UBERON:0001262!8.86e-09!13;UBERON:0004786!8.86e-09!13;UBERON:0003350!1.24e-07!9;UBERON:0004808!1.24e-07!9;UBERON:0001277!1.24e-07!9;UBERON:0002193!4.92e-07!48;UBERON:0002405!4.92e-07!48
}}

Latest revision as of 16:02, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:80289414..80289438,+p1@Oaz1
Mm9::chr17:80333927..80333940,-p@chr17:80333927..80333940
-
Mm9::chr2:121854322..121854334,+p2@Gm9781
Mm9::chr2:157727184..157727213,+p1@ENSMUST00000121302
Mm9::chr2:170110460..170110480,+p1@ENSMUST00000118388
Mm9::chr3:95231497..95231510,+p1@Gm4349
Mm9::chr3:96433842..96433878,+p1@Rbm8a
Mm9::chr7:144562355..144562367,+p@chr7:144562355..144562367
+


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:0008073ornithine decarboxylase inhibitor activity0.016159955885354
GO:0042979ornithine decarboxylase regulator activity0.016159955885354
GO:0006595polyamine metabolic process0.02584813721866
GO:0000184mRNA catabolic process, nonsense-mediated decay0.02584813721866
GO:0006402mRNA catabolic process0.0273101551622031
GO:0003729mRNA binding0.0273101551622031
GO:0006401RNA catabolic process0.0273101551622031
GO:0051028mRNA transport0.0273101551622031
GO:0050658RNA transport0.0273101551622031
GO:0051236establishment of RNA localization0.0273101551622031
GO:0050657nucleic acid transport0.0273101551622031
GO:0006403RNA localization0.0273101551622031
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0273101551622031
GO:0006576biogenic amine metabolic process0.0331823158039291
GO:0006575amino acid derivative metabolic process0.0374068710784698



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
somatic cell1.09e-17118
hematopoietic cell4.92e-1732
hematopoietic oligopotent progenitor cell4.92e-1732
hematopoietic stem cell4.92e-1732
angioblastic mesenchymal cell4.92e-1732
hematopoietic multipotent progenitor cell4.92e-1732
animal cell5.79e-16115
eukaryotic cell5.79e-16115
connective tissue cell3.95e-1546
mesenchymal cell3.95e-1546
hematopoietic lineage restricted progenitor cell7.93e-1525
epithelial cell3.13e-1425
endo-epithelial cell4.27e-1415
motile cell1.04e-1354
lymphoid lineage restricted progenitor cell4.62e-1212
mature alpha-beta T cell4.22e-119
alpha-beta T cell4.22e-119
immature T cell4.22e-119
mature T cell4.22e-119
immature alpha-beta T cell4.22e-119
endodermal cell4.99e-1120
leukocyte6.64e-1117
nongranular leukocyte6.64e-1117
T cell6.91e-1111
pro-T cell6.91e-1111
lymphocyte7.56e-1113
common lymphoid progenitor7.56e-1113
CD4-positive, alpha-beta T cell7.05e-108
stem cell8.15e-1097
nucleate cell9.68e-1016
common myeloid progenitor7.71e-0819
thymocyte8.09e-086
double negative thymocyte8.09e-086
naive T cell8.09e-086
double-positive, alpha-beta thymocyte8.09e-086
CD4-positive, alpha-beta thymocyte8.09e-086
naive thymus-derived CD4-positive, alpha-beta T cell8.09e-086
DN4 thymocyte8.09e-086
DN1 thymic pro-T cell8.09e-086
DN2 thymocyte8.09e-086
DN3 thymocyte8.09e-086
immature single positive thymocyte8.09e-086
early T lineage precursor8.09e-086
mature CD4 single-positive thymocyte8.09e-086
resting double-positive thymocyte8.09e-086
double-positive blast8.09e-086
CD69-positive double-positive thymocyte8.09e-086
CD69-positive, CD4-positive single-positive thymocyte8.09e-086
CD4-positive, CD8-intermediate double-positive thymocyte8.09e-086
CD24-positive, CD4 single-positive thymocyte8.09e-086
intestinal epithelial cell1.24e-079
epithelial cell of alimentary canal1.24e-079
somatic stem cell8.18e-0791
multi fate stem cell8.18e-0791


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)
MA0003.10.241599
MA0004.10.434673
MA0006.10.747445
MA0007.10.419994
MA0009.10.870101
MA0014.10.325341
MA0017.10.804572
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.685543
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.282934
MA0056.10
MA0057.10.31126
MA0058.10.341628
MA0059.10.353484
MA0060.11.08928
MA0061.11.19505
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.744556
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.49616
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.11.03695
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.950493
MA0103.10.307078
MA0105.11.33477
MA0106.10.626997
MA0107.12.2558
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.633896
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.11.29098
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.527241
MA0146.10.385068
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.21.36565
MA0138.20.675599
MA0002.20.513194
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.20.2464
MA0065.20.247168
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.0804339
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.11.14982
MA0161.10
MA0162.10.439322
MA0163.10.0836563
MA0164.10.551114
MA0080.20.816435
MA0018.20.560731
MA0099.20.669311
MA0079.20.431684
MA0102.21.59466
MA0258.10.60477
MA0259.10.643936
MA0442.10
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