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MCL coexpression mm9:986: Difference between revisions

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|gostat_on_MCL_coexpression=GO:0005794;Golgi apparatus;0.0275945020412737;66460,54371!GO:0006041;glucosamine metabolic process;0.0275945020412737;54371!GO:0006044;N-acetylglucosamine metabolic process;0.0275945020412737;54371!GO:0006040;amino sugar metabolic process;0.0275945020412737;54371!GO:0008146;sulfotransferase activity;0.0390632786382272;54371!GO:0016782;transferase activity, transferring sulfur-containing groups;0.0390632786382272;54371!
|gostat_on_MCL_coexpression=GO:0005794;Golgi apparatus;0.0275945020412737;66460,54371!GO:0006041;glucosamine metabolic process;0.0275945020412737;54371!GO:0006044;N-acetylglucosamine metabolic process;0.0275945020412737;54371!GO:0006040;amino sugar metabolic process;0.0275945020412737;54371!GO:0008146;sulfotransferase activity;0.0390632786382272;54371!GO:0016782;transferase activity, transferring sulfur-containing groups;0.0390632786382272;54371!
|ontology_enrichment_celltype=CL:0000221!6.99e-09!44;CL:0000133!6.99e-09!44;CL:0002319!2.10e-08!43;CL:0000117!8.88e-08!23;CL:0000337!8.88e-08!23;CL:0000055!2.52e-07!49
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!2.82e-21!54;UBERON:0001016!6.78e-21!75;UBERON:0001017!1.64e-20!73;UBERON:0001049!2.98e-20!52;UBERON:0005068!2.98e-20!52;UBERON:0006241!2.98e-20!52;UBERON:0007135!2.98e-20!52;UBERON:0000955!7.30e-18!47;UBERON:0006238!7.30e-18!47;UBERON:0002616!2.37e-17!46;UBERON:0002346!2.98e-17!64;UBERON:0003075!2.98e-17!64;UBERON:0007284!2.98e-17!64;UBERON:0004121!2.14e-16!95;UBERON:0000924!2.14e-16!95;UBERON:0006601!2.14e-16!95;UBERON:0002020!5.03e-15!34;UBERON:0010371!1.00e-14!73;UBERON:0003080!1.05e-14!40;UBERON:0002780!2.32e-14!39;UBERON:0001890!2.32e-14!39;UBERON:0006240!2.32e-14!39;UBERON:0003056!1.14e-13!49;UBERON:0003528!1.16e-12!29;UBERON:0002791!1.16e-12!29;UBERON:0001893!1.16e-12!29;UBERON:0010314!1.06e-10!92;UBERON:0000956!3.03e-09!21;UBERON:0001869!3.03e-09!21;UBERON:0000203!3.03e-09!21;UBERON:0001264!1.10e-08!12;UBERON:0002619!2.46e-08!17;UBERON:0002021!8.39e-07!10;UBERON:0000411!8.39e-07!10;UBERON:0001950!8.39e-07!10
}}
}}

Revision as of 21:33, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr2:164286731..164286784,+p3@Sys1
Mm9::chr9:95307527..95307538,-p9@Chst2
Mm9::chr9:95307603..95307610,-p8@Chst2
Mm9::chr9:95307620..95307631,-p6@Chst2
Mm9::chr9:95307646..95307658,-p4@Chst2
Mm9::chr9:95307659..95307695,-p1@Chst2
Mm9::chr9:95307700..95307718,-p3@Chst2
Mm9::chr9:95307769..95307780,-p5@Chst2


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:0005794Golgi apparatus0.0275945020412737
GO:0006041glucosamine metabolic process0.0275945020412737
GO:0006044N-acetylglucosamine metabolic process0.0275945020412737
GO:0006040amino sugar metabolic process0.0275945020412737
GO:0008146sulfotransferase activity0.0390632786382272
GO:0016782transferase activity, transferring sulfur-containing groups0.0390632786382272



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
ectodermal cell6.99e-0944
neurectodermal cell6.99e-0944
neural cell2.10e-0843
CNS neuron (sensu Vertebrata)8.88e-0823
neuroblast (sensu Vertebrata)8.88e-0823
non-terminally differentiated cell2.52e-0749

Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.82e-2154
nervous system6.78e-2175
central nervous system1.64e-2073
neural tube2.98e-2052
neural rod2.98e-2052
future spinal cord2.98e-2052
neural keel2.98e-2052
brain7.30e-1847
future brain7.30e-1847
regional part of brain2.37e-1746
neurectoderm2.98e-1764
neural plate2.98e-1764
presumptive neural plate2.98e-1764
ectoderm-derived structure2.14e-1695
ectoderm2.14e-1695
presumptive ectoderm2.14e-1695
gray matter5.03e-1534
ecto-epithelium1.00e-1473
anterior neural tube1.05e-1440
regional part of forebrain2.32e-1439
forebrain2.32e-1439
future forebrain2.32e-1439
pre-chordal neural plate1.14e-1349
brain grey matter1.16e-1229
regional part of telencephalon1.16e-1229
telencephalon1.16e-1229
structure with developmental contribution from neural crest1.06e-1092
cerebral cortex3.03e-0921
cerebral hemisphere3.03e-0921
pallium3.03e-0921
pancreas1.10e-0812
regional part of cerebral cortex2.46e-0817
occipital lobe8.39e-0710
visual cortex8.39e-0710
neocortex8.39e-0710


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)

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