Personal tools

MCL coexpression mm9:731

From FANTOM5_SSTAR

Revision as of 18:49, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Phase1 CAGE Peaks

 Short description
Mm9::chr14:13178241..13178254,-p4@Fezf2
Mm9::chr15:43701539..43701604,-p1@Tmem74
Mm9::chr18:69680960..69681007,+p10@Tcf4
Mm9::chr18:69681009..69681014,+p35@Tcf4
Mm9::chr18:69681020..69681032,+p23@Tcf4
Mm9::chr2:29108946..29109011,-p1@ENSMUST00000028141
p1@ENSMUST00000154682
Mm9::chr2:84727165..84727201,-p1@Rtn4rl2
Mm9::chr6:141473179..141473193,+p6@Slco1c1
Mm9::chr8:125276239..125276278,-p1@uc009ntp.1
Mm9::chr8:87296263..87296314,-p@chr8:87296263..87296314
-


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:0007409axonogenesis0.0165391008126874
GO:0048667neuron morphogenesis during differentiation0.0165391008126874
GO:0048812neurite morphogenesis0.0165391008126874
GO:0000904cellular morphogenesis during differentiation0.0165391008126874
GO:0031175neurite development0.0165391008126874
GO:0031103axon regeneration0.0165391008126874
GO:0031102neurite regeneration0.0165391008126874
GO:0048666neuron development0.0165391008126874
GO:0048678response to axon injury0.0165391008126874
GO:0007413axonal fasciculation0.0165391008126874
GO:0032990cell part morphogenesis0.0165391008126874
GO:0030030cell projection organization and biogenesis0.0165391008126874
GO:0048858cell projection morphogenesis0.0165391008126874
GO:0030182neuron differentiation0.0165391008126874
GO:0048699generation of neurons0.0180350152064162
GO:0031099regeneration0.0180350152064162
GO:0042246tissue regeneration0.0180350152064162
GO:0008038neuron recognition0.0180350152064162
GO:0022008neurogenesis0.0180350152064162
GO:0000902cell morphogenesis0.0298404205400454
GO:0032989cellular structure morphogenesis0.0298404205400454
GO:0016358dendrite development0.0483468890330197
GO:0007399nervous system development0.0483468890330197



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
CNS neuron (sensu Vertebrata)1.30e-1323
neuroblast (sensu Vertebrata)1.30e-1323
neuron2.44e-0733
neuronal stem cell2.44e-0733
neuroblast2.44e-0733
electrically signaling cell2.44e-0733
neuron of cerebral cortex4.65e-076

Uber Anatomy
Ontology termp-valuen
gray matter4.34e-2634
brain grey matter1.31e-2329
regional part of telencephalon1.31e-2329
telencephalon1.31e-2329
neural tube2.54e-2352
neural rod2.54e-2352
future spinal cord2.54e-2352
neural keel2.54e-2352
regional part of nervous system2.56e-2354
neurectoderm1.05e-2164
neural plate1.05e-2164
presumptive neural plate1.05e-2164
brain5.87e-2147
future brain5.87e-2147
regional part of brain4.50e-2046
pre-chordal neural plate4.52e-2049
anterior neural tube4.73e-2040
central nervous system6.98e-2073
regional part of forebrain1.16e-1939
forebrain1.16e-1939
future forebrain1.16e-1939
nervous system7.12e-1975
cerebral cortex8.15e-1921
cerebral hemisphere8.15e-1921
pallium8.15e-1921
ecto-epithelium1.03e-1773
ectoderm-derived structure4.44e-1695
ectoderm4.44e-1695
presumptive ectoderm4.44e-1695
regional part of cerebral cortex7.78e-1517
structure with developmental contribution from neural crest8.38e-1292
occipital lobe3.24e-1110
visual cortex3.24e-1110
neocortex3.24e-1110


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}}}