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MCL coexpression mm9:948: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0048536;spleen development;5.59618874327475e-05;12020,21908!GO:0048534;hemopoietic or lymphoid organ development;0.0152916525558002;12020,21908!GO:0048645;organ formation;0.0152916525558002;21908!GO:0002520;immune system development;0.0152916525558002;12020,21908!GO:0005667;transcription factor complex;0.0281699089806731;12020,21908!GO:0043565;sequence-specific DNA binding;0.0281699089806731;12020,21908!GO:0009887;organ morphogenesis;0.0281699089806731;12020,21908!GO:0044451;nucleoplasm part;0.0281699089806731;12020,21908!GO:0005654;nucleoplasm;0.0281699089806731;12020,21908!GO:0048706;embryonic skeletal development;0.0281699089806731;12020!GO:0048535;lymph node development;0.0281699089806731;21908!GO:0031981;nuclear lumen;0.0322382065132781;12020,21908!GO:0048705;skeletal morphogenesis;0.0322382065132781;12020!GO:0002376;immune system process;0.032536455815222;12020,21908!GO:0031974;membrane-enclosed lumen;0.032536455815222;12020,21908!GO:0043233;organelle lumen;0.032536455815222;12020,21908!GO:0003700;transcription factor activity;0.0368476139110079;12020,21908!
|gostat_on_MCL_coexpression=GO:0048536;spleen development;5.59618874327475e-05;12020,21908!GO:0048534;hemopoietic or lymphoid organ development;0.0152916525558002;12020,21908!GO:0048645;organ formation;0.0152916525558002;21908!GO:0002520;immune system development;0.0152916525558002;12020,21908!GO:0005667;transcription factor complex;0.0281699089806731;12020,21908!GO:0043565;sequence-specific DNA binding;0.0281699089806731;12020,21908!GO:0009887;organ morphogenesis;0.0281699089806731;12020,21908!GO:0044451;nucleoplasm part;0.0281699089806731;12020,21908!GO:0005654;nucleoplasm;0.0281699089806731;12020,21908!GO:0048706;embryonic skeletal development;0.0281699089806731;12020!GO:0048535;lymph node development;0.0281699089806731;21908!GO:0031981;nuclear lumen;0.0322382065132781;12020,21908!GO:0048705;skeletal morphogenesis;0.0322382065132781;12020!GO:0002376;immune system process;0.032536455815222;12020,21908!GO:0031974;membrane-enclosed lumen;0.032536455815222;12020,21908!GO:0043233;organelle lumen;0.032536455815222;12020,21908!GO:0003700;transcription factor activity;0.0368476139110079;12020,21908!
}}
}}

Revision as of 12:49, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr13:56803787..56803796,+p@chr13:56803787..56803796
+
Mm9::chr19:45224323..45224368,+p@chr19:45224323..45224368
+
Mm9::chr19:45224993..45225027,-p@chr19:45224993..45225027
-
Mm9::chr19:45225149..45225186,+p1@Tlx1
Mm9::chr19:45225276..45225304,+p2@Tlx1
Mm9::chr5:42099208..42099253,-p2@Rab28
Mm9::chr5:42155732..42155733,-p3@Nkx3-2
Mm9::chr5:42155788..42155800,-p1@Nkx3-2


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:0048536spleen development5.59618874327475e-05
GO:0048534hemopoietic or lymphoid organ development0.0152916525558002
GO:0048645organ formation0.0152916525558002
GO:0002520immune system development0.0152916525558002
GO:0005667transcription factor complex0.0281699089806731
GO:0043565sequence-specific DNA binding0.0281699089806731
GO:0009887organ morphogenesis0.0281699089806731
GO:0044451nucleoplasm part0.0281699089806731
GO:0005654nucleoplasm0.0281699089806731
GO:0048706embryonic skeletal development0.0281699089806731
GO:0048535lymph node development0.0281699089806731
GO:0031981nuclear lumen0.0322382065132781
GO:0048705skeletal morphogenesis0.0322382065132781
GO:0002376immune system process0.032536455815222
GO:0031974membrane-enclosed lumen0.032536455815222
GO:0043233organelle lumen0.032536455815222
GO:0003700transcription factor activity0.0368476139110079



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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