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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003080!3.09e-15!40;UBERON:0003528!3.14e-15!29;UBERON:0002791!3.14e-15!29;UBERON:0001893!3.14e-15!29;UBERON:0002780!5.24e-15!39;UBERON:0001890!5.24e-15!39;UBERON:0006240!5.24e-15!39;UBERON:0000955!1.34e-12!47;UBERON:0006238!1.34e-12!47;UBERON:0003056!8.14e-12!49;UBERON:0002616!8.51e-12!46;UBERON:0002020!1.25e-11!34;UBERON:0000956!1.62e-10!21;UBERON:0001869!1.62e-10!21;UBERON:0000203!1.62e-10!21;UBERON:0000073!7.73e-10!54;UBERON:0001049!3.15e-09!52;UBERON:0005068!3.15e-09!52;UBERON:0006241!3.15e-09!52;UBERON:0007135!3.15e-09!52;UBERON:0002619!6.47e-09!17;UBERON:0000026!4.21e-08!12;UBERON:0004708!4.21e-08!12;UBERON:0002101!4.21e-08!12;UBERON:0004357!4.21e-08!12;UBERON:0004347!4.21e-08!12;UBERON:0005732!4.21e-08!12;UBERON:0005733!4.21e-08!12;UBERON:0010707!3.30e-07!13
|ontology_enrichment_uberon=UBERON:0003080!3.09e-15!40;UBERON:0003528!3.14e-15!29;UBERON:0002791!3.14e-15!29;UBERON:0001893!3.14e-15!29;UBERON:0002780!5.24e-15!39;UBERON:0001890!5.24e-15!39;UBERON:0006240!5.24e-15!39;UBERON:0000955!1.34e-12!47;UBERON:0006238!1.34e-12!47;UBERON:0003056!8.14e-12!49;UBERON:0002616!8.51e-12!46;UBERON:0002020!1.25e-11!34;UBERON:0000956!1.62e-10!21;UBERON:0001869!1.62e-10!21;UBERON:0000203!1.62e-10!21;UBERON:0000073!7.73e-10!54;UBERON:0001049!3.15e-09!52;UBERON:0005068!3.15e-09!52;UBERON:0006241!3.15e-09!52;UBERON:0007135!3.15e-09!52;UBERON:0002619!6.47e-09!17;UBERON:0000026!4.21e-08!12;UBERON:0004708!4.21e-08!12;UBERON:0002101!4.21e-08!12;UBERON:0004357!4.21e-08!12;UBERON:0004347!4.21e-08!12;UBERON:0005732!4.21e-08!12;UBERON:0005733!4.21e-08!12;UBERON:0010707!3.30e-07!13
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.293744,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.115752,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.545768,0.489529,0.145201,0.727684,1.04384,0.537749,0.757752,0.274609,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,0.253145,0.425309,2.82585,1.00043,0.699032,0.360612,0.876199,0.401916,0.631725,0.134724,0.426986,0.4934,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.827208,0.152094,1.23259,0.257421,0.245132,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,0.0793594,3.42313,1.20595,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,1.75016,0.384901,1.03517,1.16282,2.1093,0.91226,0.631253,0.97421,0.653843,1.24825,1.23125,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.673306,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,10.0081,2.38063,1.53084,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,2.09328,1.5287,0.851091,2.18247,0.569503,1.05179,0.230371,0.416978,2.65575,0.908552,0.749664,1.26545,0.787153,1.95382,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.0513167
}}
}}

Revision as of 20:30, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr6:6812839..6812856,-p@chr6:6812839..6812856
-
Mm9::chr6:6812962..6812979,+p1@Dlx6
Mm9::chr6:6812988..6813002,+p3@Dlx6
Mm9::chr6:6813269..6813272,+p2@Dlx6
Mm9::chr6:6832076..6832092,-p1@Dlx5


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:0030326embryonic limb morphogenesis0.000258943501150261
GO:0035113embryonic appendage morphogenesis0.000258943501150261
GO:0035107appendage morphogenesis0.000258943501150261
GO:0035108limb morphogenesis0.000258943501150261
GO:0048736appendage development0.000258943501150261
GO:0060173limb development0.000258943501150261
GO:0048598embryonic morphogenesis0.0014479800732008
GO:0005667transcription factor complex0.00502663040665224
GO:0043565sequence-specific DNA binding0.00502663040665224
GO:0009790embryonic development0.00502663040665224
GO:0044451nucleoplasm part0.0062098763682065
GO:0005654nucleoplasm0.00625233833473574
GO:0031981nuclear lumen0.00815663300844468
GO:0031974membrane-enclosed lumen0.00899439116634181
GO:0043233organelle lumen0.00899439116634181
GO:0003700transcription factor activity0.0101738699893271
GO:0044428nuclear part0.0140269986754033
GO:0009653anatomical structure morphogenesis0.0172120806986589
GO:0042472inner ear morphogenesis0.0261206619311803
GO:0042471ear morphogenesis0.0275672713712403
GO:0043234protein complex0.0291253627649331
GO:0048839inner ear development0.0292299925869118
GO:0043583ear development0.0303461707032352
GO:0006355regulation of transcription, DNA-dependent0.0303461707032352
GO:0006351transcription, DNA-dependent0.0303461707032352
GO:0032774RNA biosynthetic process0.0303461707032352
GO:0003677DNA binding0.0303461707032352
GO:0045449regulation of transcription0.0303461707032352
GO:0048856anatomical structure development0.0303461707032352
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0303461707032352
GO:0006350transcription0.0303461707032352
GO:0032991macromolecular complex0.0303461707032352
GO:0010468regulation of gene expression0.0305772001889394
GO:0031323regulation of cellular metabolic process0.0321607116515682
GO:0007275multicellular organismal development0.0326616758899756
GO:0019222regulation of metabolic process0.0326616758899756
GO:0016070RNA metabolic process0.0334786777647593
GO:0044446intracellular organelle part0.0340365919858891
GO:0044422organelle part0.0340365919858891
GO:0007409axonogenesis0.0352867503015634
GO:0048667neuron morphogenesis during differentiation0.0355616341903106
GO:0048812neurite morphogenesis0.0355616341903106
GO:0000904cellular morphogenesis during differentiation0.0387104947640834
GO:0007423sensory organ development0.0387104947640834
GO:0010467gene expression0.0388094600719565
GO:0031175neurite development0.0388094600719565
GO:0003676nucleic acid binding0.0395873215100833
GO:0032502developmental process0.0407048398569286
GO:0048666neuron development0.0407048398569286
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0432173728216949
GO:0032990cell part morphogenesis0.0460040440688511
GO:0030030cell projection organization and biogenesis0.0460040440688511
GO:0048858cell projection morphogenesis0.0460040440688511
GO:0050794regulation of cellular process0.0460040440688511
GO:0030182neuron differentiation0.0460040440688511



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
anterior neural tube3.09e-1540
brain grey matter3.14e-1529
regional part of telencephalon3.14e-1529
telencephalon3.14e-1529
regional part of forebrain5.24e-1539
forebrain5.24e-1539
future forebrain5.24e-1539
brain1.34e-1247
future brain1.34e-1247
pre-chordal neural plate8.14e-1249
regional part of brain8.51e-1246
gray matter1.25e-1134
cerebral cortex1.62e-1021
cerebral hemisphere1.62e-1021
pallium1.62e-1021
regional part of nervous system7.73e-1054
neural tube3.15e-0952
neural rod3.15e-0952
future spinal cord3.15e-0952
neural keel3.15e-0952
regional part of cerebral cortex6.47e-0917
appendage4.21e-0812
paired limb/fin4.21e-0812
limb4.21e-0812
paired limb/fin bud4.21e-0812
limb bud4.21e-0812
limb/fin field4.21e-0812
limb field4.21e-0812
appendage girdle complex3.30e-0713


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}}}