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MCL coexpression mm9:2163: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0534663393899805,0,0.0308766538450896,0,0,0,0,0,0,0,0,0,0,0,0.909505371110886,0,0,0,0,0,0,0,0,0,0,0.31092318613213,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.049400930804471,0,0,0,0,0,0,0,0,0,0.0326481450697549,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0394157974199537,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.046916887530847,0,0,0,0.05268038312984,0,0,0.058973152653538,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0868501009063845,0,0.0323320383475661,0.0240677349949528,0,0,0,0,0,0,0,0,0,0,0,0.060504220684743,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.110261306845027,0.0331417600494206,0,0,0.0244872863598586,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.050487679316216,0,1.54347947995832,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0308041899510522,0,0,0,0,1.50167401797912,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.123437230911067,0.145183339048413,0.0604381279967265,0.0978461107777356,0.098117166361508,0.144251119202242,0.120670852094952,0.124973528284768,0.054819193635737,0,0.110053611258545,0.141706336142815,0,0.0298193647598867,0.113395103429383,0.101437889214316,0.092873634605593,0.0294684307081759,0.0889086222350716,0.123105517627827,0.0729583017401753,0.17704421375361,0.0553034373508932,0.096721241723504,0.0904588450746591,0.0952696640988666,0.074491100723522,0.0625582350728301,0,0.0484220980280083,0.226764784182936,0.334021854919104,0.098483738243694,0.438309357588199,0.209405341672002
|gostat_on_MCL_coexpression=GO:0042737;drug catabolic process;0.00243795540459103;18125!GO:0042738;exogenous drug catabolic process;0.00243795540459103;18125!GO:0051926;negative regulation of calcium ion transport;0.00243795540459103;18125!GO:0004517;nitric-oxide synthase activity;0.00243795540459103;18125!GO:0043267;negative regulation of potassium ion transport;0.00243795540459103;18125!GO:0002028;regulation of sodium ion transport;0.00243795540459103;18125!GO:0043271;negative regulation of ion transport;0.00243795540459103;18125!GO:0043266;regulation of potassium ion transport;0.00243795540459103;18125!GO:0051346;negative regulation of hydrolase activity;0.00243795540459103;18125!GO:0017144;drug metabolic process;0.00243795540459103;18125!GO:0051924;regulation of calcium ion transport;0.00310285233311585;18125!GO:0010181;FMN binding;0.00406325900765171;18125!GO:0050661;NADP binding;0.00412577068469251;18125!GO:0043269;regulation of ion transport;0.00417935212215604;18125!GO:0046209;nitric oxide metabolic process;0.00516272909207511;18125!GO:0006809;nitric oxide biosynthetic process;0.00516272909207511;18125!GO:0051051;negative regulation of transport;0.00516272909207511;18125!GO:0016709;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen;0.00595944654455584;18125!GO:0042383;sarcolemma;0.00696558687026008;18125!GO:0006941;striated muscle contraction;0.00696558687026008;18125!GO:0042493;response to drug;0.00696558687026008;18125!GO:0043086;negative regulation of catalytic activity;0.0104167185468889;18125!GO:0050660;FAD binding;0.0125077712061627;18125!GO:0044271;nitrogen compound biosynthetic process;0.0151695002952331;18125!GO:0003012;muscle system process;0.0151695002952331;18125!GO:0006936;muscle contraction;0.0151695002952331;18125!GO:0051049;regulation of transport;0.0151695002952331;18125!GO:0006816;calcium ion transport;0.0165485457766179;18125!GO:0005516;calmodulin binding;0.0165485457766179;18125!GO:0051336;regulation of hydrolase activity;0.0165485457766179;18125!GO:0020037;heme binding;0.0165485457766179;18125!GO:0046906;tetrapyrrole binding;0.0165485457766179;18125!GO:0006814;sodium ion transport;0.0165485457766179;18125!GO:0050662;coenzyme binding;0.0166354604077976;18125!GO:0004497;monooxygenase activity;0.0169302458652155;18125!GO:0016705;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;0.0169302458652155;18125!GO:0015674;di-, tri-valent inorganic cation transport;0.0174506281591779;18125!GO:0009055;electron carrier activity;0.0174506281591779;18125!GO:0006813;potassium ion transport;0.0191285731744834;18125!GO:0048037;cofactor binding;0.0204788253985646;18125!GO:0050790;regulation of catalytic activity;0.0317528825866246;18125!GO:0015672;monovalent inorganic cation transport;0.0332026307482397;18125!GO:0005506;iron ion binding;0.0333376227418494;18125!GO:0065009;regulation of a molecular function;0.034023022090737;18125!GO:0006118;electron transport;0.034023022090737;18125!GO:0006807;nitrogen compound metabolic process;0.0374173155574188;18125!GO:0042995;cell projection;0.0377623730753674;18125!GO:0030001;metal ion transport;0.0395151938494129;18125!GO:0044248;cellular catabolic process;0.0398849504191092;18125!GO:0006091;generation of precursor metabolites and energy;0.0398849504191092;18125!GO:0042221;response to chemical stimulus;0.0404413778879217;18125!GO:0006812;cation transport;0.0430392896425877;18125!GO:0009056;catabolic process;0.048391114823203;18125!
|gostat_on_MCL_coexpression=GO:0042737;drug catabolic process;0.00243795540459103;18125!GO:0042738;exogenous drug catabolic process;0.00243795540459103;18125!GO:0051926;negative regulation of calcium ion transport;0.00243795540459103;18125!GO:0004517;nitric-oxide synthase activity;0.00243795540459103;18125!GO:0043267;negative regulation of potassium ion transport;0.00243795540459103;18125!GO:0002028;regulation of sodium ion transport;0.00243795540459103;18125!GO:0043271;negative regulation of ion transport;0.00243795540459103;18125!GO:0043266;regulation of potassium ion transport;0.00243795540459103;18125!GO:0051346;negative regulation of hydrolase activity;0.00243795540459103;18125!GO:0017144;drug metabolic process;0.00243795540459103;18125!GO:0051924;regulation of calcium ion transport;0.00310285233311585;18125!GO:0010181;FMN binding;0.00406325900765171;18125!GO:0050661;NADP binding;0.00412577068469251;18125!GO:0043269;regulation of ion transport;0.00417935212215604;18125!GO:0046209;nitric oxide metabolic process;0.00516272909207511;18125!GO:0006809;nitric oxide biosynthetic process;0.00516272909207511;18125!GO:0051051;negative regulation of transport;0.00516272909207511;18125!GO:0016709;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen;0.00595944654455584;18125!GO:0042383;sarcolemma;0.00696558687026008;18125!GO:0006941;striated muscle contraction;0.00696558687026008;18125!GO:0042493;response to drug;0.00696558687026008;18125!GO:0043086;negative regulation of catalytic activity;0.0104167185468889;18125!GO:0050660;FAD binding;0.0125077712061627;18125!GO:0044271;nitrogen compound biosynthetic process;0.0151695002952331;18125!GO:0003012;muscle system process;0.0151695002952331;18125!GO:0006936;muscle contraction;0.0151695002952331;18125!GO:0051049;regulation of transport;0.0151695002952331;18125!GO:0006816;calcium ion transport;0.0165485457766179;18125!GO:0005516;calmodulin binding;0.0165485457766179;18125!GO:0051336;regulation of hydrolase activity;0.0165485457766179;18125!GO:0020037;heme binding;0.0165485457766179;18125!GO:0046906;tetrapyrrole binding;0.0165485457766179;18125!GO:0006814;sodium ion transport;0.0165485457766179;18125!GO:0050662;coenzyme binding;0.0166354604077976;18125!GO:0004497;monooxygenase activity;0.0169302458652155;18125!GO:0016705;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;0.0169302458652155;18125!GO:0015674;di-, tri-valent inorganic cation transport;0.0174506281591779;18125!GO:0009055;electron carrier activity;0.0174506281591779;18125!GO:0006813;potassium ion transport;0.0191285731744834;18125!GO:0048037;cofactor binding;0.0204788253985646;18125!GO:0050790;regulation of catalytic activity;0.0317528825866246;18125!GO:0015672;monovalent inorganic cation transport;0.0332026307482397;18125!GO:0005506;iron ion binding;0.0333376227418494;18125!GO:0065009;regulation of a molecular function;0.034023022090737;18125!GO:0006118;electron transport;0.034023022090737;18125!GO:0006807;nitrogen compound metabolic process;0.0374173155574188;18125!GO:0042995;cell projection;0.0377623730753674;18125!GO:0030001;metal ion transport;0.0395151938494129;18125!GO:0044248;cellular catabolic process;0.0398849504191092;18125!GO:0006091;generation of precursor metabolites and energy;0.0398849504191092;18125!GO:0042221;response to chemical stimulus;0.0404413778879217;18125!GO:0006812;cation transport;0.0430392896425877;18125!GO:0009056;catabolic process;0.048391114823203;18125!
}}
}}

Revision as of 13:08, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr15:91668686..91668696,+p2@Smgc
Mm9::chr3:113267929..113267940,-p@chr3:113267929..113267940
-
Mm9::chr5:118231026..118231084,+p2@Nos1
Mm9::chr6:132391763..132391770,-p1@uc009eje.1


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:0042737drug catabolic process0.00243795540459103
GO:0042738exogenous drug catabolic process0.00243795540459103
GO:0051926negative regulation of calcium ion transport0.00243795540459103
GO:0004517nitric-oxide synthase activity0.00243795540459103
GO:0043267negative regulation of potassium ion transport0.00243795540459103
GO:0002028regulation of sodium ion transport0.00243795540459103
GO:0043271negative regulation of ion transport0.00243795540459103
GO:0043266regulation of potassium ion transport0.00243795540459103
GO:0051346negative regulation of hydrolase activity0.00243795540459103
GO:0017144drug metabolic process0.00243795540459103
GO:0051924regulation of calcium ion transport0.00310285233311585
GO:0010181FMN binding0.00406325900765171
GO:0050661NADP binding0.00412577068469251
GO:0043269regulation of ion transport0.00417935212215604
GO:0046209nitric oxide metabolic process0.00516272909207511
GO:0006809nitric oxide biosynthetic process0.00516272909207511
GO:0051051negative regulation of transport0.00516272909207511
GO:0016709oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen0.00595944654455584
GO:0042383sarcolemma0.00696558687026008
GO:0006941striated muscle contraction0.00696558687026008
GO:0042493response to drug0.00696558687026008
GO:0043086negative regulation of catalytic activity0.0104167185468889
GO:0050660FAD binding0.0125077712061627
GO:0044271nitrogen compound biosynthetic process0.0151695002952331
GO:0003012muscle system process0.0151695002952331
GO:0006936muscle contraction0.0151695002952331
GO:0051049regulation of transport0.0151695002952331
GO:0006816calcium ion transport0.0165485457766179
GO:0005516calmodulin binding0.0165485457766179
GO:0051336regulation of hydrolase activity0.0165485457766179
GO:0020037heme binding0.0165485457766179
GO:0046906tetrapyrrole binding0.0165485457766179
GO:0006814sodium ion transport0.0165485457766179
GO:0050662coenzyme binding0.0166354604077976
GO:0004497monooxygenase activity0.0169302458652155
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.0169302458652155
GO:0015674di-, tri-valent inorganic cation transport0.0174506281591779
GO:0009055electron carrier activity0.0174506281591779
GO:0006813potassium ion transport0.0191285731744834
GO:0048037cofactor binding0.0204788253985646
GO:0050790regulation of catalytic activity0.0317528825866246
GO:0015672monovalent inorganic cation transport0.0332026307482397
GO:0005506iron ion binding0.0333376227418494
GO:0065009regulation of a molecular function0.034023022090737
GO:0006118electron transport0.034023022090737
GO:0006807nitrogen compound metabolic process0.0374173155574188
GO:0042995cell projection0.0377623730753674
GO:0030001metal ion transport0.0395151938494129
GO:0044248cellular catabolic process0.0398849504191092
GO:0006091generation of precursor metabolites and energy0.0398849504191092
GO:0042221response to chemical stimulus0.0404413778879217
GO:0006812cation transport0.0430392896425877
GO:0009056catabolic process0.048391114823203



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>disease_data<br>


Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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)

{{{tfbs_overrepresentation_jaspar}}}