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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!2.60e-16!95;UBERON:0000924!2.60e-16!95;UBERON:0006601!2.60e-16!95;UBERON:0010371!6.63e-16!73;UBERON:0000073!8.46e-16!54;UBERON:0002346!9.93e-15!64;UBERON:0003075!9.93e-15!64;UBERON:0007284!9.93e-15!64;UBERON:0001049!1.03e-14!52;UBERON:0005068!1.03e-14!52;UBERON:0006241!1.03e-14!52;UBERON:0007135!1.03e-14!52;UBERON:0001017!5.69e-14!73;UBERON:0001016!9.39e-14!75;UBERON:0002020!1.03e-13!34;UBERON:0000955!2.55e-12!47;UBERON:0006238!2.55e-12!47;UBERON:0003056!5.44e-12!49;UBERON:0002616!8.42e-12!46;UBERON:0003080!2.44e-11!40;UBERON:0003528!2.50e-11!29;UBERON:0002791!2.50e-11!29;UBERON:0001893!2.50e-11!29;UBERON:0002780!7.71e-11!39;UBERON:0001890!7.71e-11!39;UBERON:0006240!7.71e-11!39;UBERON:0010314!9.08e-11!92;UBERON:0002021!6.72e-08!10;UBERON:0000411!6.72e-08!10;UBERON:0001950!6.72e-08!10;UBERON:0000956!1.29e-07!21;UBERON:0001869!1.29e-07!21;UBERON:0000203!1.29e-07!21;UBERON:0002619!4.73e-07!17
|ontology_enrichment_uberon=UBERON:0004121!2.60e-16!95;UBERON:0000924!2.60e-16!95;UBERON:0006601!2.60e-16!95;UBERON:0010371!6.63e-16!73;UBERON:0000073!8.46e-16!54;UBERON:0002346!9.93e-15!64;UBERON:0003075!9.93e-15!64;UBERON:0007284!9.93e-15!64;UBERON:0001049!1.03e-14!52;UBERON:0005068!1.03e-14!52;UBERON:0006241!1.03e-14!52;UBERON:0007135!1.03e-14!52;UBERON:0001017!5.69e-14!73;UBERON:0001016!9.39e-14!75;UBERON:0002020!1.03e-13!34;UBERON:0000955!2.55e-12!47;UBERON:0006238!2.55e-12!47;UBERON:0003056!5.44e-12!49;UBERON:0002616!8.42e-12!46;UBERON:0003080!2.44e-11!40;UBERON:0003528!2.50e-11!29;UBERON:0002791!2.50e-11!29;UBERON:0001893!2.50e-11!29;UBERON:0002780!7.71e-11!39;UBERON:0001890!7.71e-11!39;UBERON:0006240!7.71e-11!39;UBERON:0010314!9.08e-11!92;UBERON:0002021!6.72e-08!10;UBERON:0000411!6.72e-08!10;UBERON:0001950!6.72e-08!10;UBERON:0000956!1.29e-07!21;UBERON:0001869!1.29e-07!21;UBERON:0000203!1.29e-07!21;UBERON:0002619!4.73e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.795069,0.140695,0.7433,0.329881,0.176699,0.342839,0.425757,0.345089,0.112618,3.30828,0.385334,0.414631,1.16031,0.437133,0.555819,0,0.619876,0.170475,0.656134,0.387499,0.238546,0.281622,0.436294,0.175485,0.276437,0.4628,0.0908349,0.361771,1.15025,0.0650265,0.921513,0.717576,0.504188,0.570676,0.556756,0.308746,2.88023,0.411296,0.144953,0.391645,0.173534,0.931853,0.255102,0.191571,1.45562,0.319944,0.543674,0.376103,0.208261,0.215702,1.4677,1.22385,0.220536,0.855661,0.87275,1.9733,0.223087,0.40287,0.288386,0.441884,0.698157,0.496904,0.120887,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,1.30396,0.355763,5.29776,0.905636,3.29689,0.932285,0.270351,0.532872,0.681539,0.242107,0.110993,0.636582,0.495545,0.333618,0.792744,10.3556,0.4982,0.231893,0.548334,1.51408,1.07554,0.797601,0.730003,0.181374,0.437593,0.129056,0.104462,0.732731,1.34284,0.764487,0.161581,0.717305,0.838603,0.603683,0.602672,2.51086,2.681,0.372438,0.246223,2.72214,0.781068,0.840348,0.243062,0.390066,1.0825,0.512539,2.01901,0.333247,0.621127,0.158673,0.910937,0.572279,0.464505,0.532013,1.13603,0.685116,0.433317,0.723425,1.00525,0.183744,0.821997,0.323373,0.976125,0.456508,1.10385,0.0275241,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,1.60254,2.39898,8.62531,0.857198,1.3356,0.455644,0.93735,0.488969,0.199652,0.290467,2.24847,1.06466,0.791909,0.685546,0.776587,0.593295,0.448733,0.160658,0.413167,4.33626
}}
}}

Revision as of 18:42, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr12:101758988..101759063,-p1@Ttc7b
Mm9::chr12:56922144..56922182,-p1@Ralgapa1
Mm9::chr15:36723350..36723392,-p1@Ywhaz
Mm9::chr15:76062984..76063064,-p7@Plec
Mm9::chr16:5013598..5013651,-p1@Rogdi
Mm9::chr1:59970327..59970380,+p@chr1:59970327..59970380
+
Mm9::chr3:137530722..137530761,+p1@Dnajb14
Mm9::chr5:33361418..33361419,+p7@Ywhah
Mm9::chr6:39675447..39675477,-p2@Braf
Mm9::chr9:54349372..54349451,-p1@Dmxl2
Mm9::chr9:54349454..54349490,-p2@Dmxl2


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:0019904protein domain specific binding0.0210612225400774



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)5.98e-0923
neuroblast (sensu Vertebrata)5.98e-0923
neuron6.14e-0733
neuronal stem cell6.14e-0733
neuroblast6.14e-0733
electrically signaling cell6.14e-0733

Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure2.60e-1695
ectoderm2.60e-1695
presumptive ectoderm2.60e-1695
ecto-epithelium6.63e-1673
regional part of nervous system8.46e-1654
neurectoderm9.93e-1564
neural plate9.93e-1564
presumptive neural plate9.93e-1564
neural tube1.03e-1452
neural rod1.03e-1452
future spinal cord1.03e-1452
neural keel1.03e-1452
central nervous system5.69e-1473
nervous system9.39e-1475
gray matter1.03e-1334
brain2.55e-1247
future brain2.55e-1247
pre-chordal neural plate5.44e-1249
regional part of brain8.42e-1246
anterior neural tube2.44e-1140
brain grey matter2.50e-1129
regional part of telencephalon2.50e-1129
telencephalon2.50e-1129
regional part of forebrain7.71e-1139
forebrain7.71e-1139
future forebrain7.71e-1139
structure with developmental contribution from neural crest9.08e-1192
occipital lobe6.72e-0810
visual cortex6.72e-0810
neocortex6.72e-0810
cerebral cortex1.29e-0721
cerebral hemisphere1.29e-0721
pallium1.29e-0721
regional part of cerebral cortex4.73e-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}}}