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MCL coexpression mm9:1280: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!3.86e-30!75;UBERON:0001017!2.72e-29!73;UBERON:0000073!3.87e-22!54;UBERON:0001049!8.56e-21!52;UBERON:0005068!8.56e-21!52;UBERON:0006241!8.56e-21!52;UBERON:0007135!8.56e-21!52;UBERON:0004121!3.88e-18!95;UBERON:0000924!3.88e-18!95;UBERON:0006601!3.88e-18!95;UBERON:0000955!5.28e-18!47;UBERON:0006238!5.28e-18!47;UBERON:0002616!6.79e-18!46;UBERON:0002346!7.65e-17!64;UBERON:0003075!7.65e-17!64;UBERON:0007284!7.65e-17!64;UBERON:0003080!1.63e-16!40;UBERON:0002020!2.74e-16!34;UBERON:0002780!3.37e-16!39;UBERON:0001890!3.37e-16!39;UBERON:0006240!3.37e-16!39;UBERON:0003528!1.51e-13!29;UBERON:0002791!1.51e-13!29;UBERON:0001893!1.51e-13!29;UBERON:0010314!6.01e-13!92;UBERON:0003056!7.42e-12!49;UBERON:0010371!9.24e-12!73;UBERON:0000956!7.38e-10!21;UBERON:0001869!7.38e-10!21;UBERON:0000203!7.38e-10!21;UBERON:0002619!2.23e-08!17
|ontology_enrichment_uberon=UBERON:0001016!3.86e-30!75;UBERON:0001017!2.72e-29!73;UBERON:0000073!3.87e-22!54;UBERON:0001049!8.56e-21!52;UBERON:0005068!8.56e-21!52;UBERON:0006241!8.56e-21!52;UBERON:0007135!8.56e-21!52;UBERON:0004121!3.88e-18!95;UBERON:0000924!3.88e-18!95;UBERON:0006601!3.88e-18!95;UBERON:0000955!5.28e-18!47;UBERON:0006238!5.28e-18!47;UBERON:0002616!6.79e-18!46;UBERON:0002346!7.65e-17!64;UBERON:0003075!7.65e-17!64;UBERON:0007284!7.65e-17!64;UBERON:0003080!1.63e-16!40;UBERON:0002020!2.74e-16!34;UBERON:0002780!3.37e-16!39;UBERON:0001890!3.37e-16!39;UBERON:0006240!3.37e-16!39;UBERON:0003528!1.51e-13!29;UBERON:0002791!1.51e-13!29;UBERON:0001893!1.51e-13!29;UBERON:0010314!6.01e-13!92;UBERON:0003056!7.42e-12!49;UBERON:0010371!9.24e-12!73;UBERON:0000956!7.38e-10!21;UBERON:0001869!7.38e-10!21;UBERON:0000203!7.38e-10!21;UBERON:0002619!2.23e-08!17
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.819928,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.7141,0.283981,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.143775,0.426133,0.713088,0.657163,0.345236,1.19059,0.686615,0.223823,0.572827,0.394364,0.534301,0.558142,0.960397,1.60284,0.204204,0.956447,0.144368,0.871288,0.629145,0.303703,0.752287,0.342638,0.56353,0.327433,0.366415,1.45501,0.524258,0.77511,0.589246,0.0835644,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,0.66551,0.406788,1.50238,0.21472,0.663395,0.939962,1.72013,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,1.30328,0.740068,1.156,0.208101,0.19692,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,0.768392,0.827903,1.02367,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,1.47187,0.281222,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,2.08158,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.247162,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.347287,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,2.48865,0.183562,0.667976,1.10596,0.783181,0.678689,1.18867,0.71546,0.376898,0.48935,1.25034,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.86867,0.63125,1.28815
}}
}}

Revision as of 19:40, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:120459934..120459954,+p4@Anapc11
Mm9::chr16:17530781..17530882,-p2@Thap7
Mm9::chr17:34742844..34742884,+p1@Agpat1
Mm9::chr17:36394802..36394816,-p2@Rpp21
Mm9::chr4:147514791..147514807,+p4@Mad2l2
Mm9::chr5:45911521..45911566,+p1@Med28


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:0007067mitosis0.0324891498879796
GO:0000087M phase of mitotic cell cycle0.0324891498879796
GO:0007094mitotic cell cycle spindle assembly checkpoint0.0324891498879796
GO:0031577spindle checkpoint0.0324891498879796
GO:0000278mitotic cell cycle0.0324891498879796
GO:0000279M phase0.0324891498879796
GO:0051301cell division0.0324891498879796
GO:00038411-acylglycerol-3-phosphate O-acyltransferase activity0.0324891498879796
GO:0022403cell cycle phase0.0324891498879796
GO:0004526ribonuclease P activity0.0324891498879796
GO:0004549tRNA-specific ribonuclease activity0.0324891498879796
GO:0007093mitotic cell cycle checkpoint0.0324891498879796
GO:0016411acylglycerol O-acyltransferase activity0.0324891498879796
GO:0016891endoribonuclease activity, producing 5'-phosphomonoesters0.0463685948603288
GO:0016893endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.0475920528897136



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
non-terminally differentiated cell2.09e-1949
ectodermal cell3.16e-1944
neurectodermal cell3.16e-1944
neural cell5.01e-1943
animal cell2.19e-15115
eukaryotic cell2.19e-15115
somatic cell4.23e-15118
electrically responsive cell1.62e-1339
electrically active cell1.62e-1339
neuron4.12e-1333
neuronal stem cell4.12e-1333
neuroblast4.12e-1333
electrically signaling cell4.12e-1333
embryonic cell4.62e-1270
somatic stem cell5.58e-1291
multi fate stem cell5.58e-1291
CNS neuron (sensu Vertebrata)1.07e-1123
neuroblast (sensu Vertebrata)1.07e-1123
stem cell1.51e-1097
migratory neural crest cell4.74e-0710
neuron associated cell4.74e-0710
glial cell (sensu Vertebrata)4.74e-0710
neuron associated cell (sensu Vertebrata)4.74e-0710
glial cell4.74e-0710
glioblast4.74e-0710
glioblast (sensu Vertebrata)4.74e-0710

Uber Anatomy
Ontology termp-valuen
nervous system3.86e-3075
central nervous system2.72e-2973
regional part of nervous system3.87e-2254
neural tube8.56e-2152
neural rod8.56e-2152
future spinal cord8.56e-2152
neural keel8.56e-2152
ectoderm-derived structure3.88e-1895
ectoderm3.88e-1895
presumptive ectoderm3.88e-1895
brain5.28e-1847
future brain5.28e-1847
regional part of brain6.79e-1846
neurectoderm7.65e-1764
neural plate7.65e-1764
presumptive neural plate7.65e-1764
anterior neural tube1.63e-1640
gray matter2.74e-1634
regional part of forebrain3.37e-1639
forebrain3.37e-1639
future forebrain3.37e-1639
brain grey matter1.51e-1329
regional part of telencephalon1.51e-1329
telencephalon1.51e-1329
structure with developmental contribution from neural crest6.01e-1392
pre-chordal neural plate7.42e-1249
ecto-epithelium9.24e-1273
cerebral cortex7.38e-1021
cerebral hemisphere7.38e-1021
pallium7.38e-1021
regional part of cerebral cortex2.23e-0817


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}}}