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MCL coexpression mm9:3507: Difference between revisions

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|gostat_on_MCL_coexpression=GO:0042744;hydrogen peroxide catabolic process;0.0279268370927454;13861!GO:0042743;hydrogen peroxide metabolic process;0.0279268370927454;13861!GO:0042542;response to hydrogen peroxide;0.0279268370927454;13861!GO:0000302;response to reactive oxygen species;0.0335011872033904;13861!GO:0006800;oxygen and reactive oxygen species metabolic process;0.0345159216351491;13861!GO:0004601;peroxidase activity;0.0345159216351491;13861!GO:0016684;oxidoreductase activity, acting on peroxide as acceptor;0.0345159216351491;13861!GO:0005834;heterotrimeric G-protein complex;0.0345159216351491;14693!GO:0006979;response to oxidative stress;0.0417985017757417;13861!GO:0019897;extrinsic to plasma membrane;0.0417985017757417;14693!
|gostat_on_MCL_coexpression=GO:0042744;hydrogen peroxide catabolic process;0.0279268370927454;13861!GO:0042743;hydrogen peroxide metabolic process;0.0279268370927454;13861!GO:0042542;response to hydrogen peroxide;0.0279268370927454;13861!GO:0000302;response to reactive oxygen species;0.0335011872033904;13861!GO:0006800;oxygen and reactive oxygen species metabolic process;0.0345159216351491;13861!GO:0004601;peroxidase activity;0.0345159216351491;13861!GO:0016684;oxidoreductase activity, acting on peroxide as acceptor;0.0345159216351491;13861!GO:0005834;heterotrimeric G-protein complex;0.0345159216351491;14693!GO:0006979;response to oxidative stress;0.0417985017757417;13861!GO:0019897;extrinsic to plasma membrane;0.0417985017757417;14693!
|ontology_enrichment_celltype=CL:0002321!5.58e-13!70;CL:0002319!9.30e-12!43;CL:0000221!9.32e-12!44;CL:0000133!9.32e-12!44;CL:0000055!2.51e-11!49;CL:0000117!2.45e-10!23;CL:0000337!2.45e-10!23;CL:0000540!7.18e-08!33;CL:0000047!7.18e-08!33;CL:0000031!7.18e-08!33;CL:0000404!7.18e-08!33;CL:0000393!1.48e-07!39;CL:0000211!1.48e-07!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!3.18e-13!75;UBERON:0001017!4.21e-13!73;UBERON:0002020!9.37e-13!34;UBERON:0000073!1.33e-11!54;UBERON:0002780!8.18e-11!39;UBERON:0001890!8.18e-11!39;UBERON:0006240!8.18e-11!39;UBERON:0001049!1.75e-10!52;UBERON:0005068!1.75e-10!52;UBERON:0006241!1.75e-10!52;UBERON:0007135!1.75e-10!52;UBERON:0003528!1.80e-10!29;UBERON:0002791!1.80e-10!29;UBERON:0001893!1.80e-10!29;UBERON:0003080!3.53e-10!40;UBERON:0002616!7.92e-09!46;UBERON:0000955!9.98e-09!47;UBERON:0006238!9.98e-09!47;UBERON:0004121!1.22e-08!95;UBERON:0000924!1.22e-08!95;UBERON:0006601!1.22e-08!95;UBERON:0000956!4.19e-08!21;UBERON:0001869!4.19e-08!21;UBERON:0000203!4.19e-08!21;UBERON:0002346!4.08e-07!64;UBERON:0003075!4.08e-07!64;UBERON:0007284!4.08e-07!64;UBERON:0010314!9.33e-07!92
}}
}}

Revision as of 20:10, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr5:137463371..137463439,-p1@Znhit1
Mm9::chr5:137974440..137974518,-p1@Epo
p1@Gnb2
Mm9::chr5:137974525..137974539,-p3@Gnb2


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:0042744hydrogen peroxide catabolic process0.0279268370927454
GO:0042743hydrogen peroxide metabolic process0.0279268370927454
GO:0042542response to hydrogen peroxide0.0279268370927454
GO:0000302response to reactive oxygen species0.0335011872033904
GO:0006800oxygen and reactive oxygen species metabolic process0.0345159216351491
GO:0004601peroxidase activity0.0345159216351491
GO:0016684oxidoreductase activity, acting on peroxide as acceptor0.0345159216351491
GO:0005834heterotrimeric G-protein complex0.0345159216351491
GO:0006979response to oxidative stress0.0417985017757417
GO:0019897extrinsic to plasma membrane0.0417985017757417



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>

Uber Anatomy
Ontology termp-valuen
nervous system3.18e-1375
central nervous system4.21e-1373
gray matter9.37e-1334
regional part of nervous system1.33e-1154
regional part of forebrain8.18e-1139
forebrain8.18e-1139
future forebrain8.18e-1139
neural tube1.75e-1052
neural rod1.75e-1052
future spinal cord1.75e-1052
neural keel1.75e-1052
brain grey matter1.80e-1029
regional part of telencephalon1.80e-1029
telencephalon1.80e-1029
anterior neural tube3.53e-1040
regional part of brain7.92e-0946
brain9.98e-0947
future brain9.98e-0947
ectoderm-derived structure1.22e-0895
ectoderm1.22e-0895
presumptive ectoderm1.22e-0895
cerebral cortex4.19e-0821
cerebral hemisphere4.19e-0821
pallium4.19e-0821
neurectoderm4.08e-0764
neural plate4.08e-0764
presumptive neural plate4.08e-0764
structure with developmental contribution from neural crest9.33e-0792


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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