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MCL coexpression mm9:1226: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0005681;spliceosome;0.00661407924265768;66125,20638!GO:0008380;RNA splicing;0.00661407924265768;66125,20638!GO:0006397;mRNA processing;0.00688011728768921;66125,20638!GO:0016071;mRNA metabolic process;0.00688011728768921;66125,20638!GO:0006396;RNA processing;0.00993700490759503;66125,20638!GO:0032991;macromolecular complex;0.00993700490759503;69833,66125,20638!GO:0030529;ribonucleoprotein complex;0.0107381397348516;66125,20638!GO:0016070;RNA metabolic process;0.0107381397348516;69833,66125,20638!GO:0030880;RNA polymerase complex;0.0113878965286287;69833!GO:0010467;gene expression;0.0147241541606693;69833,66125,20638!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0179963855922899;69833,66125,20638!GO:0003899;DNA-directed RNA polymerase activity;0.0223120998489921;69833!GO:0044428;nuclear part;0.0303298318377121;66125,20638!GO:0005634;nucleus;0.0342785404752569;69833,66125,20638!GO:0043283;biopolymer metabolic process;0.0350646740319669;69833,66125,20638!
|gostat_on_MCL_coexpression=GO:0005681;spliceosome;0.00661407924265768;66125,20638!GO:0008380;RNA splicing;0.00661407924265768;66125,20638!GO:0006397;mRNA processing;0.00688011728768921;66125,20638!GO:0016071;mRNA metabolic process;0.00688011728768921;66125,20638!GO:0006396;RNA processing;0.00993700490759503;66125,20638!GO:0032991;macromolecular complex;0.00993700490759503;69833,66125,20638!GO:0030529;ribonucleoprotein complex;0.0107381397348516;66125,20638!GO:0016070;RNA metabolic process;0.0107381397348516;69833,66125,20638!GO:0030880;RNA polymerase complex;0.0113878965286287;69833!GO:0010467;gene expression;0.0147241541606693;69833,66125,20638!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0179963855922899;69833,66125,20638!GO:0003899;DNA-directed RNA polymerase activity;0.0223120998489921;69833!GO:0044428;nuclear part;0.0303298318377121;66125,20638!GO:0005634;nucleus;0.0342785404752569;69833,66125,20638!GO:0043283;biopolymer metabolic process;0.0350646740319669;69833,66125,20638!
}}
}}

Revision as of 12:53, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:12728248..12728325,+p1@Sf3b5
Mm9::chr13:34254822..34254902,+p1@Psmg4
Mm9::chr15:78971754..78971788,+p1@Polr2f
Mm9::chr2:130005046..130005112,-p1@Snrpb
Mm9::chr7:133839456..133839523,+p1@Bola2
Mm9::chr8:72655226..72655291,+p1@Nr2c2ap


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:0005681spliceosome0.00661407924265768
GO:0008380RNA splicing0.00661407924265768
GO:0006397mRNA processing0.00688011728768921
GO:0016071mRNA metabolic process0.00688011728768921
GO:0006396RNA processing0.00993700490759503
GO:0032991macromolecular complex0.00993700490759503
GO:0030529ribonucleoprotein complex0.0107381397348516
GO:0016070RNA metabolic process0.0107381397348516
GO:0030880RNA polymerase complex0.0113878965286287
GO:0010467gene expression0.0147241541606693
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0179963855922899
GO:0003899DNA-directed RNA polymerase activity0.0223120998489921
GO:0044428nuclear part0.0303298318377121
GO:0005634nucleus0.0342785404752569
GO:0043283biopolymer metabolic process0.0350646740319669



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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