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MCL coexpression mm9:925: Difference between revisions

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|gostat_on_MCL_coexpression=GO:0003708;retinoic acid receptor activity;0.0390406349406792;19401!GO:0016564;transcription repressor activity;0.0390406349406792;11569,19401!GO:0055012;ventricular cardiac muscle cell differentiation;0.0390406349406792;19401!GO:0006355;regulation of transcription, DNA-dependent;0.0390406349406792;228790,11569,19401,71458!GO:0006351;transcription, DNA-dependent;0.0390406349406792;228790,11569,19401,71458!GO:0032774;RNA biosynthetic process;0.0390406349406792;228790,11569,19401,71458!GO:0045449;regulation of transcription;0.0390406349406792;228790,11569,19401,71458!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0390406349406792;228790,11569,19401,71458!GO:0006350;transcription;0.0390406349406792;228790,11569,19401,71458!GO:0055007;cardiac muscle cell differentiation;0.0390406349406792;19401!GO:0010468;regulation of gene expression;0.0390406349406792;228790,11569,19401,71458!GO:0031323;regulation of cellular metabolic process;0.0415385883410495;228790,11569,19401,71458!GO:0019222;regulation of metabolic process;0.042853123543253;228790,11569,19401,71458!GO:0016070;RNA metabolic process;0.042853123543253;228790,11569,19401,71458!GO:0035051;cardiac cell differentiation;0.042853123543253;19401!GO:0005634;nucleus;0.0459484764591356;108911,228790,11569,19401,71458!
|gostat_on_MCL_coexpression=GO:0003708;retinoic acid receptor activity;0.0390406349406792;19401!GO:0016564;transcription repressor activity;0.0390406349406792;11569,19401!GO:0055012;ventricular cardiac muscle cell differentiation;0.0390406349406792;19401!GO:0006355;regulation of transcription, DNA-dependent;0.0390406349406792;228790,11569,19401,71458!GO:0006351;transcription, DNA-dependent;0.0390406349406792;228790,11569,19401,71458!GO:0032774;RNA biosynthetic process;0.0390406349406792;228790,11569,19401,71458!GO:0045449;regulation of transcription;0.0390406349406792;228790,11569,19401,71458!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0390406349406792;228790,11569,19401,71458!GO:0006350;transcription;0.0390406349406792;228790,11569,19401,71458!GO:0055007;cardiac muscle cell differentiation;0.0390406349406792;19401!GO:0010468;regulation of gene expression;0.0390406349406792;228790,11569,19401,71458!GO:0031323;regulation of cellular metabolic process;0.0415385883410495;228790,11569,19401,71458!GO:0019222;regulation of metabolic process;0.042853123543253;228790,11569,19401,71458!GO:0016070;RNA metabolic process;0.042853123543253;228790,11569,19401,71458!GO:0035051;cardiac cell differentiation;0.042853123543253;19401!GO:0005634;nucleus;0.0459484764591356;108911,228790,11569,19401,71458!
|ontology_enrichment_celltype=CL:0000791!2.67e-07!9;CL:0000789!2.67e-07!9;CL:0002420!2.67e-07!9;CL:0002419!2.67e-07!9;CL:0000790!2.67e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002370!1.68e-07!23;UBERON:0000974!1.68e-07!23;UBERON:0004807!1.68e-07!23;UBERON:0005058!1.68e-07!23;UBERON:0003351!1.68e-07!23;UBERON:0009113!1.68e-07!23;UBERON:0003295!1.68e-07!23;UBERON:0009722!1.68e-07!23;UBERON:0005562!1.68e-07!23;UBERON:0007690!1.68e-07!23;UBERON:0006562!2.25e-07!24;UBERON:0001557!2.25e-07!24;UBERON:0001042!2.25e-07!24;UBERON:0008814!2.25e-07!24;UBERON:0009145!2.25e-07!24;UBERON:0003408!7.20e-07!24
}}
}}

Revision as of 21:28, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:98798983..98799049,+p1@Rara
Mm9::chr13:3610263..3610280,-p3@BC016423
Mm9::chr14:75347602..75347611,-p3@Lrch1
Mm9::chr2:153171907..153171931,+p4@Asxl1
Mm9::chr4:140258131..140258153,+p@chr4:140258131..140258153
+
Mm9::chr5:32439348..32439350,+p@chr5:32439348..32439350
+
Mm9::chr6:140572167..140572236,+p2@Aebp2
Mm9::chrX:11657701..11657708,-p7@Bcor


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:0003708retinoic acid receptor activity0.0390406349406792
GO:0016564transcription repressor activity0.0390406349406792
GO:0055012ventricular cardiac muscle cell differentiation0.0390406349406792
GO:0006355regulation of transcription, DNA-dependent0.0390406349406792
GO:0006351transcription, DNA-dependent0.0390406349406792
GO:0032774RNA biosynthetic process0.0390406349406792
GO:0045449regulation of transcription0.0390406349406792
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0390406349406792
GO:0006350transcription0.0390406349406792
GO:0055007cardiac muscle cell differentiation0.0390406349406792
GO:0010468regulation of gene expression0.0390406349406792
GO:0031323regulation of cellular metabolic process0.0415385883410495
GO:0019222regulation of metabolic process0.042853123543253
GO:0016070RNA metabolic process0.042853123543253
GO:0035051cardiac cell differentiation0.042853123543253
GO:0005634nucleus0.0459484764591356



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><br>

Cell Type
Ontology termp-valuen
mature alpha-beta T cell2.67e-079
alpha-beta T cell2.67e-079
immature T cell2.67e-079
mature T cell2.67e-079
immature alpha-beta T cell2.67e-079

Uber Anatomy
Ontology termp-valuen
thymus1.68e-0723
neck1.68e-0723
respiratory system epithelium1.68e-0723
hemolymphoid system gland1.68e-0723
pharyngeal epithelium1.68e-0723
thymic region1.68e-0723
pharyngeal gland1.68e-0723
entire pharyngeal arch endoderm1.68e-0723
thymus primordium1.68e-0723
early pharyngeal endoderm1.68e-0723
pharynx2.25e-0724
upper respiratory tract2.25e-0724
chordate pharynx2.25e-0724
pharyngeal arch system2.25e-0724
pharyngeal region of foregut2.25e-0724
gland of gut7.20e-0724


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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