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MCL coexpression mm9:308: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0.302135209133308,0.229760741500184,0.200524416281113,0.446923349681759,0.477639625998089,0.320048601435619,0.706451519852561,0.485250544747895,0.531998018122782,0.491046424708465,0.701094049168705,0.555174759221756,0.59222256236629,0.438689275691019,0,0.693661686986452,0.75813268863093,0.684705158062114,0.662741886197048,0.719521719249876,0,0,0.924071576217432,0.809817413802674,0.749347823200197,0.332128066466673,0.360268799800303,0.421952157331529,0.763046185951584,0.273668319951815,0.387339814683682,0.484665626237036,0,0,0.333529183982692,0.436301579848985,0.281882014776571,0.175030578462058,0.255802624898724,0.311127917657318,0.146111684480851,0.226095853111613,0.247166627096554,0.0398917015458044,0,0,0,0,0,0,0,0,0.644350202205736,0.472642480448323,0.432438101728315,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.770802699888516,0.753584159073849,0.706765268053749,0.94220190633247,0,0,0,0,0,0,0.757360503962255,0.942337068487114,0.331836684535406,0.766910181900226,0.359265182653244,0,0.821586021065555,0.881996390838138,0.843167992190059,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.386994775863171,0.660495028180615,0.414679361960878,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.399970448502024,0.672165245588183,0,0,0,0.0230059912811245,0,0,0,0,0,0,0,0,0,0,0,0.00373375308871642,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.829648550474013,0.885886861500238,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.232354270649109,0.326256291421351,0.256653413442142,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.000822852955709275,0,0,0,0,0,0,0,0,0,0,0,0,0.684428858463649,0.609142317970708,0.652967663959634,0,0,0,0,0,0,0,0,0.601965652006422,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0009055;electron carrier activity;0.0235749622765852;68194,30926!GO:0015035;protein disulfide oxidoreductase activity;0.030000362435492;30926!GO:0006118;electron transport;0.030000362435492;68194,30926!GO:0031975;envelope;0.030000362435492;69482,68194!GO:0031967;organelle envelope;0.030000362435492;69482,68194!GO:0015036;disulfide oxidoreductase activity;0.030000362435492;30926!GO:0006091;generation of precursor metabolites and energy;0.030000362435492;68194,30926!GO:0031090;organelle membrane;0.0382432531186327;69482,68194!GO:0045454;cell redox homeostasis;0.0382432531186327;30926!GO:0016491;oxidoreductase activity;0.0382432531186327;68194,30926!GO:0008137;NADH dehydrogenase (ubiquinone) activity;0.0382432531186327;68194!GO:0003954;NADH dehydrogenase activity;0.0382432531186327;68194!GO:0050136;NADH dehydrogenase (quinone) activity;0.0382432531186327;68194!GO:0051028;mRNA transport;0.0382432531186327;69482!GO:0016655;oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor;0.0382432531186327;68194!GO:0050658;RNA transport;0.0382432531186327;69482!GO:0051236;establishment of RNA localization;0.0382432531186327;69482!GO:0050657;nucleic acid transport;0.0382432531186327;69482!GO:0006403;RNA localization;0.0382432531186327;69482!GO:0005643;nuclear pore;0.0382432531186327;69482!GO:0065002;intracellular protein transport across a membrane;0.0382432531186327;69482!GO:0015931;nucleobase, nucleoside, nucleotide and nucleic acid transport;0.0382432531186327;69482!GO:0046930;pore complex;0.0382432531186327;69482!GO:0044453;nuclear membrane part;0.0395589900222561;69482!GO:0031965;nuclear membrane;0.0395589900222561;69482!GO:0016651;oxidoreductase activity, acting on NADH or NADPH;0.0398389700056067;68194!
|gostat_on_MCL_coexpression=GO:0009055;electron carrier activity;0.0235749622765852;68194,30926!GO:0015035;protein disulfide oxidoreductase activity;0.030000362435492;30926!GO:0006118;electron transport;0.030000362435492;68194,30926!GO:0031975;envelope;0.030000362435492;69482,68194!GO:0031967;organelle envelope;0.030000362435492;69482,68194!GO:0015036;disulfide oxidoreductase activity;0.030000362435492;30926!GO:0006091;generation of precursor metabolites and energy;0.030000362435492;68194,30926!GO:0031090;organelle membrane;0.0382432531186327;69482,68194!GO:0045454;cell redox homeostasis;0.0382432531186327;30926!GO:0016491;oxidoreductase activity;0.0382432531186327;68194,30926!GO:0008137;NADH dehydrogenase (ubiquinone) activity;0.0382432531186327;68194!GO:0003954;NADH dehydrogenase activity;0.0382432531186327;68194!GO:0050136;NADH dehydrogenase (quinone) activity;0.0382432531186327;68194!GO:0051028;mRNA transport;0.0382432531186327;69482!GO:0016655;oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor;0.0382432531186327;68194!GO:0050658;RNA transport;0.0382432531186327;69482!GO:0051236;establishment of RNA localization;0.0382432531186327;69482!GO:0050657;nucleic acid transport;0.0382432531186327;69482!GO:0006403;RNA localization;0.0382432531186327;69482!GO:0005643;nuclear pore;0.0382432531186327;69482!GO:0065002;intracellular protein transport across a membrane;0.0382432531186327;69482!GO:0015931;nucleobase, nucleoside, nucleotide and nucleic acid transport;0.0382432531186327;69482!GO:0046930;pore complex;0.0382432531186327;69482!GO:0044453;nuclear membrane part;0.0395589900222561;69482!GO:0031965;nuclear membrane;0.0395589900222561;69482!GO:0016651;oxidoreductase activity, acting on NADH or NADPH;0.0398389700056067;68194!
}}
}}

Revision as of 12:39, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:28749875..28749924,+p@chr10:28749875..28749924
+
Mm9::chr10:43243886..43243899,+p2@ENSMUST00000057649
Mm9::chr12:24587988..24588001,+p@chr12:24587988..24588001
+
Mm9::chr12:70223961..70223973,+p@chr12:70223961..70223973
+
Mm9::chr13:118018159..118018169,+p@chr13:118018159..118018169
+
Mm9::chr14:28023521..28023536,+p@chr14:28023521..28023536
+
Mm9::chr15:81296769..81296795,+p1@Gm9840
p1@Rbx1
Mm9::chr17:47547801..47547833,+p@chr17:47547801..47547833
+
Mm9::chr18:38873969..38873988,+p@chr18:38873969..38873988
+
Mm9::chr19:25107619..25107626,+p@chr19:25107619..25107626
+
Mm9::chr19:28838027..28838030,-p1@Gm6788
Mm9::chr1:13426571..13426575,+p@chr1:13426571..13426575
+
Mm9::chr1:15057084..15057123,+p@chr1:15057084..15057123
+
Mm9::chr2:150131486..150131493,+p1@ENSMUST00000120921
Mm9::chr2:36244522..36244568,+p1@ENSMUST00000121366
Mm9::chr2:52475255..52475266,+p2@Bloc1s2
p2@Gm13540
Mm9::chr2:80479001..80479013,+p3@Nup35
Mm9::chr4:116821517..116821519,+p1@ENSMUST00000118674
Mm9::chr4:34432983..34433015,+p2@ENSMUST00000117487
Mm9::chr7:144629334..144629355,+p1@Gm12669
Mm9::chr7:3181067..3181081,+p@chr7:3181067..3181081
+
Mm9::chr7:54087766..54087785,+p2@Gm5331
Mm9::chr7:54087805..54087833,+p1@Gm5331
Mm9::chr9:120293968..120293975,+p1@ENSMUST00000118890
Mm9::chr9:48258428..48258437,+p5@Gm5616
p5@LOC100045968
p5@LOC100505330
p5@Nhp2l1
Mm9::chrX:101543820..101543838,-p1@ENSMUST00000120233


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:0009055electron carrier activity0.0235749622765852
GO:0015035protein disulfide oxidoreductase activity0.030000362435492
GO:0006118electron transport0.030000362435492
GO:0031975envelope0.030000362435492
GO:0031967organelle envelope0.030000362435492
GO:0015036disulfide oxidoreductase activity0.030000362435492
GO:0006091generation of precursor metabolites and energy0.030000362435492
GO:0031090organelle membrane0.0382432531186327
GO:0045454cell redox homeostasis0.0382432531186327
GO:0016491oxidoreductase activity0.0382432531186327
GO:0008137NADH dehydrogenase (ubiquinone) activity0.0382432531186327
GO:0003954NADH dehydrogenase activity0.0382432531186327
GO:0050136NADH dehydrogenase (quinone) activity0.0382432531186327
GO:0051028mRNA transport0.0382432531186327
GO:0016655oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor0.0382432531186327
GO:0050658RNA transport0.0382432531186327
GO:0051236establishment of RNA localization0.0382432531186327
GO:0050657nucleic acid transport0.0382432531186327
GO:0006403RNA localization0.0382432531186327
GO:0005643nuclear pore0.0382432531186327
GO:0065002intracellular protein transport across a membrane0.0382432531186327
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0382432531186327
GO:0046930pore complex0.0382432531186327
GO:0044453nuclear membrane part0.0395589900222561
GO:0031965nuclear membrane0.0395589900222561
GO:0016651oxidoreductase activity, acting on NADH or NADPH0.0398389700056067



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)

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