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MCL coexpression mm9:1237: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.83e-23!54;UBERON:0001049!2.75e-23!52;UBERON:0005068!2.75e-23!52;UBERON:0006241!2.75e-23!52;UBERON:0007135!2.75e-23!52;UBERON:0002346!1.23e-21!64;UBERON:0003075!1.23e-21!64;UBERON:0007284!1.23e-21!64;UBERON:0002020!5.65e-21!34;UBERON:0001017!6.63e-20!73;UBERON:0001016!6.77e-19!75;UBERON:0000955!9.79e-19!47;UBERON:0006238!9.79e-19!47;UBERON:0010371!1.84e-18!73;UBERON:0002616!4.24e-18!46;UBERON:0003056!1.86e-17!49;UBERON:0003080!3.02e-17!40;UBERON:0002780!2.08e-16!39;UBERON:0001890!2.08e-16!39;UBERON:0006240!2.08e-16!39;UBERON:0003528!2.80e-16!29;UBERON:0002791!2.80e-16!29;UBERON:0001893!2.80e-16!29;UBERON:0004121!4.88e-16!95;UBERON:0000924!4.88e-16!95;UBERON:0006601!4.88e-16!95;UBERON:0010314!5.49e-15!92;UBERON:0000956!1.13e-09!21;UBERON:0001869!1.13e-09!21;UBERON:0000203!1.13e-09!21;UBERON:0002420!2.31e-08!8;UBERON:0007245!2.31e-08!8;UBERON:0010009!2.31e-08!8;UBERON:0010011!2.31e-08!8;UBERON:0000454!2.31e-08!8;UBERON:0002619!3.31e-07!17
|ontology_enrichment_uberon=UBERON:0000073!1.83e-23!54;UBERON:0001049!2.75e-23!52;UBERON:0005068!2.75e-23!52;UBERON:0006241!2.75e-23!52;UBERON:0007135!2.75e-23!52;UBERON:0002346!1.23e-21!64;UBERON:0003075!1.23e-21!64;UBERON:0007284!1.23e-21!64;UBERON:0002020!5.65e-21!34;UBERON:0001017!6.63e-20!73;UBERON:0001016!6.77e-19!75;UBERON:0000955!9.79e-19!47;UBERON:0006238!9.79e-19!47;UBERON:0010371!1.84e-18!73;UBERON:0002616!4.24e-18!46;UBERON:0003056!1.86e-17!49;UBERON:0003080!3.02e-17!40;UBERON:0002780!2.08e-16!39;UBERON:0001890!2.08e-16!39;UBERON:0006240!2.08e-16!39;UBERON:0003528!2.80e-16!29;UBERON:0002791!2.80e-16!29;UBERON:0001893!2.80e-16!29;UBERON:0004121!4.88e-16!95;UBERON:0000924!4.88e-16!95;UBERON:0006601!4.88e-16!95;UBERON:0010314!5.49e-15!92;UBERON:0000956!1.13e-09!21;UBERON:0001869!1.13e-09!21;UBERON:0000203!1.13e-09!21;UBERON:0002420!2.31e-08!8;UBERON:0007245!2.31e-08!8;UBERON:0010009!2.31e-08!8;UBERON:0010011!2.31e-08!8;UBERON:0000454!2.31e-08!8;UBERON:0002619!3.31e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.473747,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,0.0835344,0.599767,0.632897,0.692139,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.86893,0.426133,0.108444,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,0.394364,0.534301,0.558142,0.960397,0.336199,0.589948,0.364821,0.144368,0.326478,0.629145,0.820134,0.27383,0.342638,0.56353,0.327433,0.366415,0.161543,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,1.77235,1.156,0.208101,0.57254,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,0.439832,0.827903,0.534643,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.810643,0.281222,0.685716,0.976308,0.775372,0.160254,0.871473,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,1.10269,0.605144,1.33732,0.340765,0.0704207,0.53982,0.858327,0.862623,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,2.32117,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,1.10885,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.86867,0.63125,0.0323861
}}
}}

Revision as of 19:36, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:20672299..20672310,+p5@Ahi1
Mm9::chr16:72027752..72027771,+p@chr16:72027752..72027771
+
Mm9::chr17:48015995..48016037,-p12@Foxp4
Mm9::chr2:178062247..178062272,+p5@Phactr3
Mm9::chr2:32178983..32179012,-p@chr2:32178983..32179012
-
Mm9::chr5:137972432..137972464,-p15@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:0048617embryonic foregut morphogenesis0.0274254607533146
GO:0007440foregut morphogenesis0.0274254607533146
GO:0048613embryonic ectodermal gut morphogenesis0.0274254607533146
GO:0048611embryonic ectodermal gut development0.0274254607533146
GO:0048558embryonic gut morphogenesis0.0274254607533146
GO:0048557embryonic digestive tract morphogenesis0.0274254607533146
GO:0007439ectodermal gut development0.0274254607533146
GO:0048567ectodermal gut morphogenesis0.0274254607533146
GO:0048547gut morphogenesis0.0274254607533146
GO:0048566embryonic gut development0.0274254607533146
GO:0048546digestive tract morphogenesis0.0274254607533146
GO:0004864protein phosphatase inhibitor activity0.0309339166018306
GO:0048565gut development0.031478544579051
GO:0019212phosphatase inhibitor activity0.031478544579051
GO:0048562embryonic organ morphogenesis0.0324672658235487
GO:0019888protein phosphatase regulator activity0.0449732511525825
GO:0005834heterotrimeric G-protein complex0.0449732511525825
GO:0019208phosphatase regulator activity0.0450415573124482
GO:0048568embryonic organ development0.0451018725408811



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)3.18e-1923
neuroblast (sensu Vertebrata)3.18e-1923
neuron1.23e-1133
neuronal stem cell1.23e-1133
neuroblast1.23e-1133
electrically signaling cell1.23e-1133
electrically responsive cell1.45e-0839
electrically active cell1.45e-0839
ectodermal cell2.85e-0744
neurectodermal cell2.85e-0744
neural cell4.78e-0743

Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.83e-2354
neural tube2.75e-2352
neural rod2.75e-2352
future spinal cord2.75e-2352
neural keel2.75e-2352
neurectoderm1.23e-2164
neural plate1.23e-2164
presumptive neural plate1.23e-2164
gray matter5.65e-2134
central nervous system6.63e-2073
nervous system6.77e-1975
brain9.79e-1947
future brain9.79e-1947
ecto-epithelium1.84e-1873
regional part of brain4.24e-1846
pre-chordal neural plate1.86e-1749
anterior neural tube3.02e-1740
regional part of forebrain2.08e-1639
forebrain2.08e-1639
future forebrain2.08e-1639
brain grey matter2.80e-1629
regional part of telencephalon2.80e-1629
telencephalon2.80e-1629
ectoderm-derived structure4.88e-1695
ectoderm4.88e-1695
presumptive ectoderm4.88e-1695
structure with developmental contribution from neural crest5.49e-1592
cerebral cortex1.13e-0921
cerebral hemisphere1.13e-0921
pallium1.13e-0921
basal ganglion2.31e-088
nuclear complex of neuraxis2.31e-088
aggregate regional part of brain2.31e-088
collection of basal ganglia2.31e-088
cerebral subcortex2.31e-088
regional part of cerebral cortex3.31e-0717


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}}}