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MCL coexpression mm9:196: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.434704241352084,0.225301871178984,0.187437010020026,0.469723258307596,0.510563029767974,0.354876380541933,0,0,0,0,0,0,0,0,0,0,0.468513623788752,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.19106458117176,0,0,0,0,0,0,0,0,0.10536076625968,0,0.137398724818722,0.210606173730573,0.442174267268086,0.567139480176429,0.590469675984498,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.034489466458534,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0050381;unspecific monooxygenase activity;0.000381407618093475;13087,53973,13086!GO:0004497;monooxygenase activity;0.000381407618093475;14262,13087,53973,13086!GO:0016705;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;0.000381407618093475;14262,13087,53973,13086!GO:0016712;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen;0.000381407618093475;13087,53973,13086!GO:0005792;microsome;0.000526622955370677;14262,13087,53973,13086!GO:0042598;vesicular fraction;0.000526622955370677;14262,13087,53973,13086!GO:0005624;membrane fraction;0.00162387099983086;14262,13087,53973,21816,13086!GO:0000267;cell fraction;0.00235617037791491;14262,13087,53973,21816,13086!GO:0020037;heme binding;0.00384637371565087;13087,53973,13086!GO:0046906;tetrapyrrole binding;0.00384637371565087;13087,53973,13086!GO:0006118;electron transport;0.00428262213647489;14262,13087,53973,13086!GO:0006091;generation of precursor metabolites and energy;0.0107482932718783;14262,13087,53973,13086!GO:0047685;amine sulfotransferase activity;0.0197017139437564;57430!GO:0032789;unsaturated monocarboxylic acid metabolic process;0.032001252598815;171281!GO:0032788;saturated monocarboxylic acid metabolic process;0.032001252598815;171281!GO:0015501;glutamate:sodium symporter activity;0.032001252598815;20511!GO:0005506;iron ion binding;0.0383846732732145;13087,53973,13086!GO:0050832;defense response to fungus;0.0383846732732145;66438!GO:0004813;alanine-tRNA ligase activity;0.0383846732732145;234734!GO:0006419;alanyl-tRNA aminoacylation;0.0383846732732145;234734!GO:0005783;endoplasmic reticulum;0.0399510662243412;14262,13087,53973,13086!GO:0015813;L-glutamate transport;0.0465064880593034;20511!GO:0016491;oxidoreductase activity;0.049463534248198;14262,13087,53973,13086!GO:0004499;flavin-containing monooxygenase activity;0.049463534248198;14262!GO:0015800;acidic amino acid transport;0.049463534248198;20511!GO:0005313;L-glutamate transmembrane transporter activity;0.049463534248198;20511!GO:0015172;acidic amino acid transmembrane transporter activity;0.049463534248198;20511!GO:0003810;protein-glutamine gamma-glutamyltransferase activity;0.049463534248198;21816!GO:0018149;peptide cross-linking;0.049463534248198;21816!GO:0005283;sodium:amino acid symporter activity;0.049463534248198;20511!GO:0000038;very-long-chain fatty acid metabolic process;0.049463534248198;171281!
|gostat_on_MCL_coexpression=GO:0050381;unspecific monooxygenase activity;0.000381407618093475;13087,53973,13086!GO:0004497;monooxygenase activity;0.000381407618093475;14262,13087,53973,13086!GO:0016705;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;0.000381407618093475;14262,13087,53973,13086!GO:0016712;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen;0.000381407618093475;13087,53973,13086!GO:0005792;microsome;0.000526622955370677;14262,13087,53973,13086!GO:0042598;vesicular fraction;0.000526622955370677;14262,13087,53973,13086!GO:0005624;membrane fraction;0.00162387099983086;14262,13087,53973,21816,13086!GO:0000267;cell fraction;0.00235617037791491;14262,13087,53973,21816,13086!GO:0020037;heme binding;0.00384637371565087;13087,53973,13086!GO:0046906;tetrapyrrole binding;0.00384637371565087;13087,53973,13086!GO:0006118;electron transport;0.00428262213647489;14262,13087,53973,13086!GO:0006091;generation of precursor metabolites and energy;0.0107482932718783;14262,13087,53973,13086!GO:0047685;amine sulfotransferase activity;0.0197017139437564;57430!GO:0032789;unsaturated monocarboxylic acid metabolic process;0.032001252598815;171281!GO:0032788;saturated monocarboxylic acid metabolic process;0.032001252598815;171281!GO:0015501;glutamate:sodium symporter activity;0.032001252598815;20511!GO:0005506;iron ion binding;0.0383846732732145;13087,53973,13086!GO:0050832;defense response to fungus;0.0383846732732145;66438!GO:0004813;alanine-tRNA ligase activity;0.0383846732732145;234734!GO:0006419;alanyl-tRNA aminoacylation;0.0383846732732145;234734!GO:0005783;endoplasmic reticulum;0.0399510662243412;14262,13087,53973,13086!GO:0015813;L-glutamate transport;0.0465064880593034;20511!GO:0016491;oxidoreductase activity;0.049463534248198;14262,13087,53973,13086!GO:0004499;flavin-containing monooxygenase activity;0.049463534248198;14262!GO:0015800;acidic amino acid transport;0.049463534248198;20511!GO:0005313;L-glutamate transmembrane transporter activity;0.049463534248198;20511!GO:0015172;acidic amino acid transmembrane transporter activity;0.049463534248198;20511!GO:0003810;protein-glutamine gamma-glutamyltransferase activity;0.049463534248198;21816!GO:0018149;peptide cross-linking;0.049463534248198;21816!GO:0005283;sodium:amino acid symporter activity;0.049463534248198;20511!GO:0000038;very-long-chain fatty acid metabolic process;0.049463534248198;171281!
}}
}}

Revision as of 12:38, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:33506521..33506543,-p@chr10:33506521..33506543
-
Mm9::chr10:33570806..33570810,+p@chr10:33570806..33570810
+
Mm9::chr10:33577516..33577519,+p1@Sult3a1
Mm9::chr10:79785781..79785791,-p10@Pcsk4
Mm9::chr12:73729820..73729827,-p@chr12:73729820..73729827
-
Mm9::chr12:80867845..80867864,+p@chr12:80867845..80867864
+
Mm9::chr12:80867869..80867911,+p@chr12:80867869..80867911
+
Mm9::chr12:85383465..85383477,+p@chr12:85383465..85383477
+
Mm9::chr12:85394299..85394333,+p@chr12:85394299..85394333
+
Mm9::chr13:35085097..35085115,-p7@Eci2
Mm9::chr14:56331943..56331947,-p2@Tgm1
Mm9::chr15:58876086..58876093,-p@chr15:58876086..58876093
-
Mm9::chr15:60752835..60752843,-p1@A1bg
Mm9::chr17:3463010..3463040,+p@chr17:3463010..3463040
+
Mm9::chr18:64639037..64639046,-p@chr18:64639037..64639046
-
Mm9::chr19:39961157..39961185,-p2@Cyp2c69
Mm9::chr19:39961220..39961250,-p1@Cyp2c69
Mm9::chr19:7876675..7876690,-p@chr19:7876675..7876690
-
Mm9::chr19:7877136..7877156,-p1@Slc22a26
Mm9::chr19:7877159..7877170,-p2@Slc22a26
Mm9::chr19:7877174..7877180,-p3@Slc22a26
Mm9::chr1:164914650..164914664,-p1@Fmo3
Mm9::chr1:191995926..191995933,+p@chr1:191995926..191995933
+
Mm9::chr1:36837940..36837957,+p@chr1:36837940..36837957
+
Mm9::chr1:89921716..89921733,+p1@ENSMUST00000119510
Mm9::chr1:90062579..90062612,+p1@Ugt1a5
Mm9::chr2:102546571..102546587,+p7@Slc1a2
Mm9::chr2:147872720..147872727,-p9@Foxa2
Mm9::chr2:34734962..34734966,+p@chr2:34734962..34734966
+
Mm9::chr2:5597037..5597071,-p4@Camk1d
Mm9::chr3:133454457..133454466,-p@chr3:133454457..133454466
-
Mm9::chr3:133454479..133454487,-p@chr3:133454479..133454487
-
Mm9::chr4:108811262..108811268,-p@chr4:108811262..108811268
-
Mm9::chr4:122648733..122648736,+p@chr4:122648733..122648736
+
Mm9::chr4:127199683..127199694,+p@chr4:127199683..127199694
+
Mm9::chr4:98697506..98697517,-p@chr4:98697506..98697517
-
Mm9::chr5:146345592..146345596,-p1@Cyp3a41a
p1@Cyp3a41b
Mm9::chr5:146531700..146531712,-p2@Cyp3a41a
p2@Cyp3a41b
Mm9::chr7:148237545..148237575,+p@chr7:148237545..148237575
+
Mm9::chr7:20278257..20278260,-p5@Apoc1
Mm9::chr7:26884144..26884148,+p@chr7:26884144..26884148
+
Mm9::chr7:27092210..27092216,+p1@Cyp2a4
Mm9::chr7:27620356..27620362,+p1@Cyp2a5
Mm9::chr7:31709188..31709204,-p1@Hamp2
Mm9::chr8:113560802..113560812,+p@chr8:113560802..113560812
+
Mm9::chr8:91106679..91106681,+p@chr8:91106679..91106681
+
Mm9::chr9:21639933..21639948,+p1@Gm6484
Mm9::chr9:21640079..21640090,+p@chr9:21640079..21640090
+
Mm9::chrX:20126832..20126843,+p2@Rgn


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:0050381unspecific monooxygenase activity0.000381407618093475
GO:0004497monooxygenase activity0.000381407618093475
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.000381407618093475
GO:0016712oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen0.000381407618093475
GO:0005792microsome0.000526622955370677
GO:0042598vesicular fraction0.000526622955370677
GO:0005624membrane fraction0.00162387099983086
GO:0000267cell fraction0.00235617037791491
GO:0020037heme binding0.00384637371565087
GO:0046906tetrapyrrole binding0.00384637371565087
GO:0006118electron transport0.00428262213647489
GO:0006091generation of precursor metabolites and energy0.0107482932718783
GO:0047685amine sulfotransferase activity0.0197017139437564
GO:0032789unsaturated monocarboxylic acid metabolic process0.032001252598815
GO:0032788saturated monocarboxylic acid metabolic process0.032001252598815
GO:0015501glutamate:sodium symporter activity0.032001252598815
GO:0005506iron ion binding0.0383846732732145
GO:0050832defense response to fungus0.0383846732732145
GO:0004813alanine-tRNA ligase activity0.0383846732732145
GO:0006419alanyl-tRNA aminoacylation0.0383846732732145
GO:0005783endoplasmic reticulum0.0399510662243412
GO:0015813L-glutamate transport0.0465064880593034
GO:0016491oxidoreductase activity0.049463534248198
GO:0004499flavin-containing monooxygenase activity0.049463534248198
GO:0015800acidic amino acid transport0.049463534248198
GO:0005313L-glutamate transmembrane transporter activity0.049463534248198
GO:0015172acidic amino acid transmembrane transporter activity0.049463534248198
GO:0003810protein-glutamine gamma-glutamyltransferase activity0.049463534248198
GO:0018149peptide cross-linking0.049463534248198
GO:0005283sodium:amino acid symporter activity0.049463534248198
GO:0000038very-long-chain fatty acid metabolic process0.049463534248198



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}}}

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