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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!1.13e-28!64;UBERON:0003075!1.13e-28!64;UBERON:0007284!1.13e-28!64;UBERON:0003056!6.49e-25!49;UBERON:0010371!1.63e-23!73;UBERON:0004121!1.57e-22!95;UBERON:0000924!1.57e-22!95;UBERON:0006601!1.57e-22!95;UBERON:0001049!2.60e-18!52;UBERON:0005068!2.60e-18!52;UBERON:0006241!2.60e-18!52;UBERON:0007135!2.60e-18!52;UBERON:0001016!1.17e-17!75;UBERON:0001017!2.85e-17!73;UBERON:0000073!5.01e-16!54;UBERON:0010314!5.26e-16!92;UBERON:0003080!1.59e-14!40;UBERON:0000955!6.18e-14!47;UBERON:0006238!6.18e-14!47;UBERON:0002780!7.28e-14!39;UBERON:0001890!7.28e-14!39;UBERON:0006240!7.28e-14!39;UBERON:0002020!1.64e-13!34;UBERON:0000970!1.87e-13!9;UBERON:0000019!1.87e-13!9;UBERON:0000047!1.87e-13!9;UBERON:0010312!1.87e-13!9;UBERON:0004088!1.87e-13!9;UBERON:0002104!1.87e-13!9;UBERON:0001456!1.87e-13!9;UBERON:0003072!1.87e-13!9;UBERON:0004128!1.87e-13!9;UBERON:0003071!1.87e-13!9;UBERON:0002616!6.77e-13!46;UBERON:0001444!1.57e-10!11;UBERON:0000020!1.93e-09!12;UBERON:0001032!1.93e-09!12;UBERON:0004456!1.93e-09!12;UBERON:0003528!6.04e-09!29;UBERON:0002791!6.04e-09!29;UBERON:0001893!6.04e-09!29;UBERON:0000033!1.60e-08!13;UBERON:0005085!1.60e-08!13;UBERON:0002240!5.58e-08!6;UBERON:0005174!5.58e-08!6;UBERON:0001137!5.58e-08!6;UBERON:0001948!3.38e-07!5;UBERON:0002315!3.38e-07!5
|ontology_enrichment_uberon=UBERON:0002346!1.13e-28!64;UBERON:0003075!1.13e-28!64;UBERON:0007284!1.13e-28!64;UBERON:0003056!6.49e-25!49;UBERON:0010371!1.63e-23!73;UBERON:0004121!1.57e-22!95;UBERON:0000924!1.57e-22!95;UBERON:0006601!1.57e-22!95;UBERON:0001049!2.60e-18!52;UBERON:0005068!2.60e-18!52;UBERON:0006241!2.60e-18!52;UBERON:0007135!2.60e-18!52;UBERON:0001016!1.17e-17!75;UBERON:0001017!2.85e-17!73;UBERON:0000073!5.01e-16!54;UBERON:0010314!5.26e-16!92;UBERON:0003080!1.59e-14!40;UBERON:0000955!6.18e-14!47;UBERON:0006238!6.18e-14!47;UBERON:0002780!7.28e-14!39;UBERON:0001890!7.28e-14!39;UBERON:0006240!7.28e-14!39;UBERON:0002020!1.64e-13!34;UBERON:0000970!1.87e-13!9;UBERON:0000019!1.87e-13!9;UBERON:0000047!1.87e-13!9;UBERON:0010312!1.87e-13!9;UBERON:0004088!1.87e-13!9;UBERON:0002104!1.87e-13!9;UBERON:0001456!1.87e-13!9;UBERON:0003072!1.87e-13!9;UBERON:0004128!1.87e-13!9;UBERON:0003071!1.87e-13!9;UBERON:0002616!6.77e-13!46;UBERON:0001444!1.57e-10!11;UBERON:0000020!1.93e-09!12;UBERON:0001032!1.93e-09!12;UBERON:0004456!1.93e-09!12;UBERON:0003528!6.04e-09!29;UBERON:0002791!6.04e-09!29;UBERON:0001893!6.04e-09!29;UBERON:0000033!1.60e-08!13;UBERON:0005085!1.60e-08!13;UBERON:0002240!5.58e-08!6;UBERON:0005174!5.58e-08!6;UBERON:0001137!5.58e-08!6;UBERON:0001948!3.38e-07!5;UBERON:0002315!3.38e-07!5
|tfbs_overrepresentation_for_novel_motifs=0.557864,1.02681,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.115752,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.775038,1.0421,0.489529,0.44579,0.727684,0.404661,1.32977,0.757752,0.274609,0.641282,0.456327,0.227599,0.626183,1.03545,1.02297,0.704734,0.425309,0.791367,1.00043,0.699032,0.360612,0.328675,0.401916,0.631725,0.134724,0.426986,0.0637209,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,1.18377,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,1.49829,0.46305,1.23259,0.257421,0.686172,1.30151,0.835925,0.997094,0.494135,0.830212,0.948899,0.794502,0.293164,1.1148,0.574099,0.618102,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.806207,1.05152,0.848095,0.20438,1.7727,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.328405,1.47653,0.932233,0.991416,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,1.72039,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.867604,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,0.416978,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.425122
}}
}}

Revision as of 19:59, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:119129106..119129125,+p@chr10:119129106..119129125
+
Mm9::chr10:119129451..119129463,+p@chr10:119129451..119129463
+
Mm9::chr10:36226819..36226830,+p6@Hs3st5
Mm9::chr1:89079885..89079891,+p1@Prss56
Mm9::chr2:105523125..105523134,+p10@Pax6


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:0021902commitment of a neuronal cell to a specific type of neuron in the forebrain0.0081630416917767
GO:0021877forebrain neuron fate commitment0.0081630416917767
GO:0009950dorsal/ventral axis specification0.0122428853841288
GO:0021798forebrain dorsal/ventral pattern formation0.0122428853841288
GO:0008467heparin-glucosamine 3-O-sulfotransferase activity0.0122428853841288
GO:0022612gland morphogenesis0.0122428853841288
GO:0021871forebrain regionalization0.0122428853841288
GO:0007435salivary gland morphogenesis0.0122428853841288
GO:0021879forebrain neuron differentiation0.0126959777294741
GO:0021872generation of neurons in the forebrain0.0130583621575619
GO:0007431salivary gland development0.0154123204435505
GO:0021543pallium development0.0154123204435505
GO:0035272exocrine system development0.0154123204435505
GO:0042462eye photoreceptor cell development0.0154123204435505
GO:0045665negative regulation of neuron differentiation0.0154123204435505
GO:0001754eye photoreceptor cell differentiation0.0154123204435505
GO:0009798axis specification0.0154123204435505
GO:0042461photoreceptor cell development0.0154123204435505
GO:0021983pituitary gland development0.0154596129039684
GO:0021536diencephalon development0.0155754504481163
GO:0048663neuron fate commitment0.0155754504481163
GO:0046530photoreceptor cell differentiation0.0155754504481163
GO:0021537telencephalon development0.0163157968418642
GO:0001709cell fate determination0.0163157968418642
GO:0045664regulation of neuron differentiation0.017619611528558
GO:0009953dorsal/ventral pattern formation0.0253030419031981
GO:0048592eye morphogenesis0.0253030419031981
GO:0008146sulfotransferase activity0.0253030419031981
GO:0050767regulation of neurogenesis0.0253030419031981
GO:0035270endocrine system development0.0260881008947712
GO:0016782transferase activity, transferring sulfur-containing groups0.0264928204051225
GO:0030334regulation of cell migration0.0264928204051225
GO:0001764neuron migration0.0271698872877182
GO:0051270regulation of cell motility0.0282855429741964
GO:0040012regulation of locomotion0.0293370380011564
GO:0048732gland development0.0330263261225084
GO:0043010camera-type eye development0.0330263261225084
GO:0007411axon guidance0.0338685444371027
GO:0045596negative regulation of cell differentiation0.0355006099299734
GO:0009952anterior/posterior pattern formation0.0382685514432561
GO:0030900forebrain development0.0384800415206376
GO:0045165cell fate commitment0.0384800415206376
GO:0001654eye development0.0384800415206376
GO:0051093negative regulation of developmental process0.0384800415206376
GO:0008285negative regulation of cell proliferation0.0426734051288919



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)8.80e-1123
neuroblast (sensu Vertebrata)8.80e-1123
neuron2.38e-0833
neuronal stem cell2.38e-0833
neuroblast2.38e-0833
electrically signaling cell2.38e-0833

Uber Anatomy
Ontology termp-valuen
neurectoderm1.13e-2864
neural plate1.13e-2864
presumptive neural plate1.13e-2864
pre-chordal neural plate6.49e-2549
ecto-epithelium1.63e-2373
ectoderm-derived structure1.57e-2295
ectoderm1.57e-2295
presumptive ectoderm1.57e-2295
neural tube2.60e-1852
neural rod2.60e-1852
future spinal cord2.60e-1852
neural keel2.60e-1852
nervous system1.17e-1775
central nervous system2.85e-1773
regional part of nervous system5.01e-1654
structure with developmental contribution from neural crest5.26e-1692
anterior neural tube1.59e-1440
brain6.18e-1447
future brain6.18e-1447
regional part of forebrain7.28e-1439
forebrain7.28e-1439
future forebrain7.28e-1439
gray matter1.64e-1334
eye1.87e-139
camera-type eye1.87e-139
simple eye1.87e-139
immature eye1.87e-139
ocular region1.87e-139
visual system1.87e-139
face1.87e-139
optic cup1.87e-139
optic vesicle1.87e-139
eye primordium1.87e-139
regional part of brain6.77e-1346
subdivision of head1.57e-1011
sense organ1.93e-0912
sensory system1.93e-0912
entire sense organ system1.93e-0912
brain grey matter6.04e-0929
regional part of telencephalon6.04e-0929
telencephalon6.04e-0929
head1.60e-0813
ectodermal placode1.60e-0813
spinal cord5.58e-086
dorsal region element5.58e-086
dorsum5.58e-086
regional part of spinal cord3.38e-075
gray matter of spinal cord3.38e-075


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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