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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002020!2.94e-13!34;UBERON:0000064!1.86e-12!99;UBERON:0003528!1.12e-11!29;UBERON:0002791!1.12e-11!29;UBERON:0001893!1.12e-11!29;UBERON:0000956!6.12e-11!21;UBERON:0001869!6.12e-11!21;UBERON:0000203!6.12e-11!21;UBERON:0001016!1.26e-10!75;UBERON:0000073!1.40e-10!54;UBERON:0001017!1.96e-10!73;UBERON:0001049!4.30e-10!52;UBERON:0005068!4.30e-10!52;UBERON:0006241!4.30e-10!52;UBERON:0007135!4.30e-10!52;UBERON:0004121!1.57e-09!95;UBERON:0000924!1.57e-09!95;UBERON:0006601!1.57e-09!95;UBERON:0000955!4.29e-09!47;UBERON:0006238!4.29e-09!47;UBERON:0002780!1.05e-08!39;UBERON:0001890!1.05e-08!39;UBERON:0006240!1.05e-08!39;UBERON:0002619!1.07e-08!17;UBERON:0003080!1.22e-08!40;UBERON:0010371!1.24e-08!73;UBERON:0002616!1.44e-08!46;UBERON:0002021!4.47e-08!10;UBERON:0000411!4.47e-08!10;UBERON:0001950!4.47e-08!10;UBERON:0002346!4.80e-08!64;UBERON:0003075!4.80e-08!64;UBERON:0007284!4.80e-08!64
|ontology_enrichment_uberon=UBERON:0002020!2.94e-13!34;UBERON:0000064!1.86e-12!99;UBERON:0003528!1.12e-11!29;UBERON:0002791!1.12e-11!29;UBERON:0001893!1.12e-11!29;UBERON:0000956!6.12e-11!21;UBERON:0001869!6.12e-11!21;UBERON:0000203!6.12e-11!21;UBERON:0001016!1.26e-10!75;UBERON:0000073!1.40e-10!54;UBERON:0001017!1.96e-10!73;UBERON:0001049!4.30e-10!52;UBERON:0005068!4.30e-10!52;UBERON:0006241!4.30e-10!52;UBERON:0007135!4.30e-10!52;UBERON:0004121!1.57e-09!95;UBERON:0000924!1.57e-09!95;UBERON:0006601!1.57e-09!95;UBERON:0000955!4.29e-09!47;UBERON:0006238!4.29e-09!47;UBERON:0002780!1.05e-08!39;UBERON:0001890!1.05e-08!39;UBERON:0006240!1.05e-08!39;UBERON:0002619!1.07e-08!17;UBERON:0003080!1.22e-08!40;UBERON:0010371!1.24e-08!73;UBERON:0002616!1.44e-08!46;UBERON:0002021!4.47e-08!10;UBERON:0000411!4.47e-08!10;UBERON:0001950!4.47e-08!10;UBERON:0002346!4.80e-08!64;UBERON:0003075!4.80e-08!64;UBERON:0007284!4.80e-08!64
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.564138,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,1.138,0.328717,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,2.02463,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.156582,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,1.83166,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,1.62246,0.195254,1.75916,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,1.38502,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,2.74838,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.609576,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,1.79943,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.999018,0.721422,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.421338
}}
}}

Revision as of 21:34, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:13685585..13685645,+p2@Hivep2
Mm9::chr10:13685899..13685916,+p1@Hivep2
Mm9::chrX:12339216..12339239,-p4@Med14


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:0044451nucleoplasm part0.0202373801242691
GO:0005654nucleoplasm0.0202373801242691
GO:0031981nuclear lumen0.0202373801242691
GO:0031974membrane-enclosed lumen0.0202373801242691
GO:0043233organelle lumen0.0202373801242691
GO:0000119mediator complex0.0241471748558044
GO:0044428nuclear part0.0255491761587703
GO:0016591DNA-directed RNA polymerase II, holoenzyme0.0414820964828024
GO:0043234protein complex0.0414820964828024
GO:0003713transcription coactivator activity0.0414820964828024
GO:0006355regulation of transcription, DNA-dependent0.0414820964828024
GO:0006351transcription, DNA-dependent0.0414820964828024
GO:0032774RNA biosynthetic process0.0414820964828024
GO:0045449regulation of transcription0.0414820964828024
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0414820964828024
GO:0006350transcription0.0414820964828024
GO:0032991macromolecular complex0.0414820964828024
GO:0010468regulation of gene expression0.0414820964828024
GO:0031323regulation of cellular metabolic process0.0414820964828024
GO:0019222regulation of metabolic process0.0414820964828024
GO:0016070RNA metabolic process0.0414820964828024
GO:0003712transcription cofactor activity0.0414820964828024
GO:0044446intracellular organelle part0.0414820964828024
GO:0044422organelle part0.0414820964828024
GO:0016563transcription activator activity0.0483065873043917
GO:0008134transcription factor binding0.0483065873043917
GO:0010467gene expression0.0483065873043917
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0483065873043917



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
neuron3.12e-0733
neuronal stem cell3.12e-0733
neuroblast3.12e-0733
electrically signaling cell3.12e-0733

Uber Anatomy
Ontology termp-valuen
gray matter2.94e-1334
organ part1.86e-1299
brain grey matter1.12e-1129
regional part of telencephalon1.12e-1129
telencephalon1.12e-1129
cerebral cortex6.12e-1121
cerebral hemisphere6.12e-1121
pallium6.12e-1121
nervous system1.26e-1075
regional part of nervous system1.40e-1054
central nervous system1.96e-1073
neural tube4.30e-1052
neural rod4.30e-1052
future spinal cord4.30e-1052
neural keel4.30e-1052
ectoderm-derived structure1.57e-0995
ectoderm1.57e-0995
presumptive ectoderm1.57e-0995
brain4.29e-0947
future brain4.29e-0947
regional part of forebrain1.05e-0839
forebrain1.05e-0839
future forebrain1.05e-0839
regional part of cerebral cortex1.07e-0817
anterior neural tube1.22e-0840
ecto-epithelium1.24e-0873
regional part of brain1.44e-0846
occipital lobe4.47e-0810
visual cortex4.47e-0810
neocortex4.47e-0810
neurectoderm4.80e-0864
neural plate4.80e-0864
presumptive neural plate4.80e-0864


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}}}