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MCL coexpression mm9:473: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0005634;nucleus;0.0474044833244923;72154,224694,243308,432508,109151,22688,71389,70208!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0474044833244923;22688,71389,232339,70208,209584,432508,109151!GO:0016070;RNA metabolic process;0.0474044833244923;22688,232339,70208,209584,432508,109151!GO:0003682;chromatin binding;0.0474044833244923;71389,109151!GO:0004386;helicase activity;0.0474044833244923;71389,109151!GO:0006333;chromatin assembly or disassembly;0.0474044833244923;71389,109151!GO:0010467;gene expression;0.0474044833244923;22688,232339,70208,209584,432508,109151!GO:0006355;regulation of transcription, DNA-dependent;0.0474044833244923;22688,232339,70208,432508,109151!GO:0006351;transcription, DNA-dependent;0.0474044833244923;22688,232339,70208,432508,109151!GO:0032774;RNA biosynthetic process;0.0474044833244923;22688,232339,70208,432508,109151!GO:0003677;DNA binding;0.0474044833244923;22688,71389,232339,432508,109151!GO:0045449;regulation of transcription;0.0474044833244923;22688,232339,70208,432508,109151!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0474044833244923;22688,232339,70208,432508,109151!GO:0006350;transcription;0.0474044833244923;22688,232339,70208,432508,109151!
|gostat_on_MCL_coexpression=GO:0005634;nucleus;0.0474044833244923;72154,224694,243308,432508,109151,22688,71389,70208!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0474044833244923;22688,71389,232339,70208,209584,432508,109151!GO:0016070;RNA metabolic process;0.0474044833244923;22688,232339,70208,209584,432508,109151!GO:0003682;chromatin binding;0.0474044833244923;71389,109151!GO:0004386;helicase activity;0.0474044833244923;71389,109151!GO:0006333;chromatin assembly or disassembly;0.0474044833244923;71389,109151!GO:0010467;gene expression;0.0474044833244923;22688,232339,70208,209584,432508,109151!GO:0006355;regulation of transcription, DNA-dependent;0.0474044833244923;22688,232339,70208,432508,109151!GO:0006351;transcription, DNA-dependent;0.0474044833244923;22688,232339,70208,432508,109151!GO:0032774;RNA biosynthetic process;0.0474044833244923;22688,232339,70208,432508,109151!GO:0003677;DNA binding;0.0474044833244923;22688,71389,232339,432508,109151!GO:0045449;regulation of transcription;0.0474044833244923;22688,232339,70208,432508,109151!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0474044833244923;22688,232339,70208,432508,109151!GO:0006350;transcription;0.0474044833244923;22688,232339,70208,432508,109151!
}}
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Revision as of 12:42, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:116814011..116814034,-p1@Cpsf6
Mm9::chr10:24589804..24589856,+p1@Med23
Mm9::chr17:33170312..33170356,-p1@Zfp763
Mm9::chr17:33495777..33495831,-p1@Zfp81
Mm9::chr18:25327494..25327530,+p1@AW554918
Mm9::chr2:160934772..160934827,-p1@Chd6
Mm9::chr2:37298793..37298859,+p1@Rabgap1
Mm9::chr3:154260009..154260052,-p1@Tyw3
Mm9::chr5:138882699..138882758,+p1@Zfp157
Mm9::chr5:139064066..139064121,+p1@A430033K04Rik
Mm9::chr6:118512244..118512298,-p1@Ankrd26
Mm9::chr7:46807844..46807882,+p@chr7:46807844..46807882
+
Mm9::chr8:93478822..93478958,+p1@Chd9
Mm9::chr9:20264394..20264448,-p1@Zfp26
Mm9::chr9:82869014..82869073,-p1@Phip


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:0005634nucleus0.0474044833244923
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0474044833244923
GO:0016070RNA metabolic process0.0474044833244923
GO:0003682chromatin binding0.0474044833244923
GO:0004386helicase activity0.0474044833244923
GO:0006333chromatin assembly or disassembly0.0474044833244923
GO:0010467gene expression0.0474044833244923
GO:0006355regulation of transcription, DNA-dependent0.0474044833244923
GO:0006351transcription, DNA-dependent0.0474044833244923
GO:0032774RNA biosynthetic process0.0474044833244923
GO:0003677DNA binding0.0474044833244923
GO:0045449regulation of transcription0.0474044833244923
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0474044833244923
GO:0006350transcription0.0474044833244923



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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