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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003056!4.78e-34!49;UBERON:0003080!2.26e-24!40;UBERON:0002346!5.14e-24!64;UBERON:0003075!5.14e-24!64;UBERON:0007284!5.14e-24!64;UBERON:0002780!1.04e-23!39;UBERON:0001890!1.04e-23!39;UBERON:0006240!1.04e-23!39;UBERON:0003528!3.54e-23!29;UBERON:0002791!3.54e-23!29;UBERON:0001893!3.54e-23!29;UBERON:0000955!4.24e-22!47;UBERON:0006238!4.24e-22!47;UBERON:0004121!4.62e-22!95;UBERON:0000924!4.62e-22!95;UBERON:0006601!4.62e-22!95;UBERON:0010371!1.29e-21!73;UBERON:0002616!2.58e-21!46;UBERON:0001017!1.11e-18!73;UBERON:0000073!1.51e-18!54;UBERON:0002020!2.62e-18!34;UBERON:0000956!3.13e-18!21;UBERON:0001869!3.13e-18!21;UBERON:0000203!3.13e-18!21;UBERON:0001016!8.75e-18!75;UBERON:0001049!1.92e-17!52;UBERON:0005068!1.92e-17!52;UBERON:0006241!1.92e-17!52;UBERON:0007135!1.92e-17!52;UBERON:0002619!5.58e-14!17;UBERON:0010314!5.77e-14!92;UBERON:0000020!1.19e-10!12;UBERON:0001032!1.19e-10!12;UBERON:0004456!1.19e-10!12;UBERON:0000970!1.73e-10!9;UBERON:0000019!1.73e-10!9;UBERON:0000047!1.73e-10!9;UBERON:0010312!1.73e-10!9;UBERON:0004088!1.73e-10!9;UBERON:0002104!1.73e-10!9;UBERON:0001456!1.73e-10!9;UBERON:0003072!1.73e-10!9;UBERON:0004128!1.73e-10!9;UBERON:0003071!1.73e-10!9;UBERON:0000033!1.48e-09!13;UBERON:0005085!1.48e-09!13;UBERON:0001444!4.53e-08!11;UBERON:0002021!6.09e-08!10;UBERON:0000411!6.09e-08!10;UBERON:0001950!6.09e-08!10;UBERON:0001954!1.53e-07!7;UBERON:0003022!1.53e-07!7;UBERON:0002421!1.53e-07!7;UBERON:0000349!1.53e-07!7;UBERON:0002600!1.53e-07!7
|ontology_enrichment_uberon=UBERON:0003056!4.78e-34!49;UBERON:0003080!2.26e-24!40;UBERON:0002346!5.14e-24!64;UBERON:0003075!5.14e-24!64;UBERON:0007284!5.14e-24!64;UBERON:0002780!1.04e-23!39;UBERON:0001890!1.04e-23!39;UBERON:0006240!1.04e-23!39;UBERON:0003528!3.54e-23!29;UBERON:0002791!3.54e-23!29;UBERON:0001893!3.54e-23!29;UBERON:0000955!4.24e-22!47;UBERON:0006238!4.24e-22!47;UBERON:0004121!4.62e-22!95;UBERON:0000924!4.62e-22!95;UBERON:0006601!4.62e-22!95;UBERON:0010371!1.29e-21!73;UBERON:0002616!2.58e-21!46;UBERON:0001017!1.11e-18!73;UBERON:0000073!1.51e-18!54;UBERON:0002020!2.62e-18!34;UBERON:0000956!3.13e-18!21;UBERON:0001869!3.13e-18!21;UBERON:0000203!3.13e-18!21;UBERON:0001016!8.75e-18!75;UBERON:0001049!1.92e-17!52;UBERON:0005068!1.92e-17!52;UBERON:0006241!1.92e-17!52;UBERON:0007135!1.92e-17!52;UBERON:0002619!5.58e-14!17;UBERON:0010314!5.77e-14!92;UBERON:0000020!1.19e-10!12;UBERON:0001032!1.19e-10!12;UBERON:0004456!1.19e-10!12;UBERON:0000970!1.73e-10!9;UBERON:0000019!1.73e-10!9;UBERON:0000047!1.73e-10!9;UBERON:0010312!1.73e-10!9;UBERON:0004088!1.73e-10!9;UBERON:0002104!1.73e-10!9;UBERON:0001456!1.73e-10!9;UBERON:0003072!1.73e-10!9;UBERON:0004128!1.73e-10!9;UBERON:0003071!1.73e-10!9;UBERON:0000033!1.48e-09!13;UBERON:0005085!1.48e-09!13;UBERON:0001444!4.53e-08!11;UBERON:0002021!6.09e-08!10;UBERON:0000411!6.09e-08!10;UBERON:0001950!6.09e-08!10;UBERON:0001954!1.53e-07!7;UBERON:0003022!1.53e-07!7;UBERON:0002421!1.53e-07!7;UBERON:0000349!1.53e-07!7;UBERON:0002600!1.53e-07!7
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.0206456,0.330161,0.394491,0.645379,0.40827,1.24018,0.146465,0.154135,0.573183,0.453212,0.484001,0.146657,0.507558,0.24249,0,1.66303,0.62892,0.134657,0.247067,0.296085,0.179861,0.50668,0.226287,0.337218,0.534339,0.128175,0.428336,0.268347,0.656973,0.414842,0.796599,0.218674,0.735537,0.242923,0.00999634,0.210533,0.480503,0.191662,0.167387,0.637027,0.419787,0.663794,0.684206,0.0122159,0.383899,0.618203,0.443479,0.314152,0.271021,0.679429,0.560572,0.0915709,0.937018,0.954342,0.514504,0.279148,0.471658,0.12126,0.512521,1.8289,0.569793,0.492158,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.840217,0.460931,0.191038,0.987652,0.116281,0.107966,0.364033,0.607043,0.759798,0.299972,0.152219,0.713779,0.568383,0.436063,0.873141,0.395495,0.0211263,0.657454,0.623015,1.60001,1.15927,0.878077,0.809272,0.657661,0.188213,0.17334,0.14449,0.812053,0.618454,0.0816605,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,1.11973,0.30446,0.806647,3.41859,0.921485,0.301014,1.15983,1.16629,0.222515,0.496288,0.398075,0.697928,0.597328,0.993019,0.647706,0.536114,0.606154,2.73257,1.8014,0.503569,0.802564,2.4656,0.235546,0.90286,0.387557,1.05894,0.527782,1.18781,2.04509,0.362565,2.83137,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.229209,0.098204,0.369078,0.938577,0.178329,0.526881,1.01974,0.561556,0.253271,0.352329,0.362302,1.1483,0.872292,0.763895,3.4055,0.669337,0.519673,1.1358,0.482466,0.683949
}}
}}

Revision as of 18:52, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:42303385..42303401,-p1@Nr2e1
Mm9::chr10:42303410..42303422,-p3@Nr2e1
Mm9::chr10:42303434..42303445,-p4@Nr2e1
Mm9::chr10:42303452..42303470,-p2@Nr2e1
Mm9::chr10:42303593..42303617,+p3@Ostm1
Mm9::chr13:100214377..100214396,-p5@Mtap1b
Mm9::chr13:100214398..100214443,-p4@Mtap1b
Mm9::chr15:30387382..30387465,+p@chr15:30387382..30387465
+
Mm9::chr4:154335024..154335039,+p1@Hes5


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:0045665negative regulation of neuron differentiation0.000794495253785691
GO:0045664regulation of neuron differentiation0.000838742615128936
GO:0030182neuron differentiation0.000838742615128936
GO:0048699generation of neurons0.00091378028845023
GO:0022008neurogenesis0.00091378028845023
GO:0048731system development0.00163346912530473
GO:0048869cellular developmental process0.00163346912530473
GO:0030154cell differentiation0.00163346912530473
GO:0048856anatomical structure development0.00235172011241831
GO:0045596negative regulation of cell differentiation0.00235172011241831
GO:0007399nervous system development0.00251666452717617
GO:0045165cell fate commitment0.00251666452717617
GO:0007275multicellular organismal development0.00251666452717617
GO:0051093negative regulation of developmental process0.00251666452717617
GO:0021960anterior commissure morphogenesis0.00268814258843295
GO:0045595regulation of cell differentiation0.00476361711834936
GO:0032502developmental process0.00537390981097135
GO:0007423sensory organ development0.00537390981097135
GO:0021988olfactory lobe development0.00537390981097135
GO:0042668auditory receptor cell fate determination0.00537390981097135
GO:0021772olfactory bulb development0.00537390981097135
GO:0008347glial cell migration0.00537390981097135
GO:0031175neurite development0.00537390981097135
GO:0048666neuron development0.00625326153862338
GO:0048468cell development0.00625326153862338
GO:0060120inner ear receptor cell fate commitment0.00719801520321865
GO:0009912auditory receptor cell fate commitment0.00719801520321865
GO:0021952central nervous system projection neuron axonogenesis0.00719801520321865
GO:0050793regulation of developmental process0.00721312630204343
GO:0032990cell part morphogenesis0.00721312630204343
GO:0048858cell projection morphogenesis0.00721312630204343
GO:0030030cell projection organization and biogenesis0.00721312630204343
GO:0048513organ development0.00801501860859627
GO:0005519cytoskeletal regulatory protein binding0.00829752406539178
GO:0021987cerebral cortex development0.00895532164740805
GO:0035176social behavior0.00895532164740805
GO:0001578microtubule bundle formation0.00915266077810837
GO:0060041retina development in camera-type eye0.00915266077810837
GO:0021955central nervous system neuron axonogenesis0.00915266077810837
GO:0005829cytosol0.00915266077810837
GO:0032501multicellular organismal process0.00988022014933451
GO:0021543pallium development0.0131141185809079
GO:0016439tRNA-pseudouridine synthase activity0.0131141185809079
GO:0000902cell morphogenesis0.0150329301666908
GO:0032989cellular structure morphogenesis0.0150329301666908
GO:0009982pseudouridine synthase activity0.0157561972414516
GO:0030316osteoclast differentiation0.0171315822530225
GO:0021954central nervous system neuron development0.0176119602344722
GO:0051705behavioral interaction between organisms0.0180725959911146
GO:0042491auditory receptor cell differentiation0.0181516412460269
GO:0021537telencephalon development0.0181516412460269
GO:0021953central nervous system neuron differentiation0.0182245960741205
GO:0001709cell fate determination0.0182245960741205
GO:0060113inner ear receptor cell differentiation0.0201180295317525
GO:0016866intramolecular transferase activity0.0212118888217189
GO:0042490mechanoreceptor differentiation0.0236988425884903
GO:0016358dendrite development0.0275027898001106
GO:0002573myeloid leukocyte differentiation0.0277193658618234
GO:0042063gliogenesis0.0279284885099959
GO:0005496steroid binding0.0309506211559055
GO:0003707steroid hormone receptor activity0.0309506211559055
GO:0004879ligand-dependent nuclear receptor activity0.031096763193158
GO:0048523negative regulation of cellular process0.0330922663318068
GO:0048519negative regulation of biological process0.037446062826476
GO:0000226microtubule cytoskeleton organization and biogenesis0.039496706719972
GO:0048839inner ear development0.0425239977973949
GO:0048469cell maturation0.0441397823276559
GO:0043010camera-type eye development0.0441397823276559
GO:0043583ear development0.0441397823276559



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)6.92e-0923
neuroblast (sensu Vertebrata)6.92e-0923
ectodermal cell2.56e-0844
neurectodermal cell2.56e-0844
neuron of cerebral cortex3.86e-086
neural cell1.19e-0743

Uber Anatomy
Ontology termp-valuen
pre-chordal neural plate4.78e-3449
anterior neural tube2.26e-2440
neurectoderm5.14e-2464
neural plate5.14e-2464
presumptive neural plate5.14e-2464
regional part of forebrain1.04e-2339
forebrain1.04e-2339
future forebrain1.04e-2339
brain grey matter3.54e-2329
regional part of telencephalon3.54e-2329
telencephalon3.54e-2329
brain4.24e-2247
future brain4.24e-2247
ectoderm-derived structure4.62e-2295
ectoderm4.62e-2295
presumptive ectoderm4.62e-2295
ecto-epithelium1.29e-2173
regional part of brain2.58e-2146
central nervous system1.11e-1873
regional part of nervous system1.51e-1854
gray matter2.62e-1834
cerebral cortex3.13e-1821
cerebral hemisphere3.13e-1821
pallium3.13e-1821
nervous system8.75e-1875
neural tube1.92e-1752
neural rod1.92e-1752
future spinal cord1.92e-1752
neural keel1.92e-1752
regional part of cerebral cortex5.58e-1417
structure with developmental contribution from neural crest5.77e-1492
sense organ1.19e-1012
sensory system1.19e-1012
entire sense organ system1.19e-1012
eye1.73e-109
camera-type eye1.73e-109
simple eye1.73e-109
immature eye1.73e-109
ocular region1.73e-109
visual system1.73e-109
face1.73e-109
optic cup1.73e-109
optic vesicle1.73e-109
eye primordium1.73e-109
head1.48e-0913
ectodermal placode1.48e-0913
subdivision of head4.53e-0811
occipital lobe6.09e-0810
visual cortex6.09e-0810
neocortex6.09e-0810
Ammon's horn1.53e-077
lobe parts of cerebral cortex1.53e-077
hippocampal formation1.53e-077
limbic system1.53e-077
limbic lobe1.53e-077


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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