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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002780!5.62e-15!39;UBERON:0001890!5.62e-15!39;UBERON:0006240!5.62e-15!39;UBERON:0000955!1.80e-14!47;UBERON:0006238!1.80e-14!47;UBERON:0003080!1.88e-14!40;UBERON:0002616!2.71e-13!46;UBERON:0003056!5.22e-13!49;UBERON:0003528!2.10e-12!29;UBERON:0002791!2.10e-12!29;UBERON:0001893!2.10e-12!29;UBERON:0000073!1.72e-11!54;UBERON:0001049!4.68e-11!52;UBERON:0005068!4.68e-11!52;UBERON:0006241!4.68e-11!52;UBERON:0007135!4.68e-11!52;UBERON:0002020!6.18e-10!34;UBERON:0000369!7.56e-10!5;UBERON:0002435!7.56e-10!5;UBERON:0000204!7.56e-10!5;UBERON:0010082!7.56e-10!5;UBERON:0002346!1.33e-09!64;UBERON:0003075!1.33e-09!64;UBERON:0007284!1.33e-09!64;UBERON:0001017!7.15e-08!73;UBERON:0002420!7.36e-08!8;UBERON:0007245!7.36e-08!8;UBERON:0010009!7.36e-08!8;UBERON:0010011!7.36e-08!8;UBERON:0000454!7.36e-08!8;UBERON:0010371!1.18e-07!73;UBERON:0001016!1.69e-07!75;UBERON:0001954!7.27e-07!7;UBERON:0003022!7.27e-07!7;UBERON:0002421!7.27e-07!7;UBERON:0000349!7.27e-07!7;UBERON:0002600!7.27e-07!7
|ontology_enrichment_uberon=UBERON:0002780!5.62e-15!39;UBERON:0001890!5.62e-15!39;UBERON:0006240!5.62e-15!39;UBERON:0000955!1.80e-14!47;UBERON:0006238!1.80e-14!47;UBERON:0003080!1.88e-14!40;UBERON:0002616!2.71e-13!46;UBERON:0003056!5.22e-13!49;UBERON:0003528!2.10e-12!29;UBERON:0002791!2.10e-12!29;UBERON:0001893!2.10e-12!29;UBERON:0000073!1.72e-11!54;UBERON:0001049!4.68e-11!52;UBERON:0005068!4.68e-11!52;UBERON:0006241!4.68e-11!52;UBERON:0007135!4.68e-11!52;UBERON:0002020!6.18e-10!34;UBERON:0000369!7.56e-10!5;UBERON:0002435!7.56e-10!5;UBERON:0000204!7.56e-10!5;UBERON:0010082!7.56e-10!5;UBERON:0002346!1.33e-09!64;UBERON:0003075!1.33e-09!64;UBERON:0007284!1.33e-09!64;UBERON:0001017!7.15e-08!73;UBERON:0002420!7.36e-08!8;UBERON:0007245!7.36e-08!8;UBERON:0010009!7.36e-08!8;UBERON:0010011!7.36e-08!8;UBERON:0000454!7.36e-08!8;UBERON:0010371!1.18e-07!73;UBERON:0001016!1.69e-07!75;UBERON:0001954!7.27e-07!7;UBERON:0003022!7.27e-07!7;UBERON:0002421!7.27e-07!7;UBERON:0000349!7.27e-07!7;UBERON:0002600!7.27e-07!7
|tfbs_overrepresentation_for_novel_motifs=1.53306,0.221337,1.36862,0.411965,0.725975,0.234508,0.675307,0.0240095,0.0286607,0.883969,1.2753,0.156123,1.31972,0.178347,0.00243098,0,0.399663,0.0904111,0.0434464,0.420889,0.577766,0.0152609,0.177495,0.0399774,0.487408,0.786209,0.860798,0.495219,0.471927,1.11587,0.0990629,0.183906,0.0880249,0.170894,1.41073,0.0802409,2.14109,0.988067,0.0222432,0.263396,0.318713,1.52476,0.0102986,0.0157107,0.788999,0.387046,2.11562,1.66477,0.0940713,0.987107,0.757286,0.0655278,0.251701,0.760373,1.43687,0.413912,0.00456687,0.954455,0.0309639,0.410216,0.512044,0.891917,0.75179,0.112645,0.759959,1.33444,0.393152,0.692274,0.169183,0.561562,0.413173,0.208292,8.46737,0.314307,2.01842,2.83869,0.265123,1.49643,0.161936,0.0337819,0.123394,0.422908,0.241704,0.776317,0.658123,0.854278,1.21325,3.23409,0.305282,1.96251,0.44947,0.665883,0.560088,0.205897,3.45118,0.0930375,0.0541546,0.564259,0.622856,0.0189994,0.276464,0.183736,2.8902,0.118492,1.80341,0.472636,0.456397,0.118042,7.66936,0.847253,0.307043,0.266353,0.597263,0.133363,1.15354,0.313651,0.94288,0.687473,0.401389,0.15237,0.318309,0.102664,0.0566365,2.05187,0.500504,0.953901,1.52328,0.187574,0.39195,0.211845,0.253351,0.0801222,1.71678,0.438966,0.473194,0.94061,0.338633,0.254041,1.10472,1.19378,0.811996,0.396892,0.219399,0.190296,0.74184,0.25263,0.0905195,1.15529,0.34357,0.0417621,1.65252,2.93096,0.278483,0.100862,0.197568,0.338479,0.234185,0.13447,0.157674,0.567238,0.440436,0.656791,0.493371,1.10427,0.113143,0.190296,0.273286,0.0395815,0.51423
}}
}}

Revision as of 17:56, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr12:109150430..109150441,-p@chr12:109150430..109150441
-
Mm9::chr14:22807636..22807658,-p@chr14:22807636..22807658
-
Mm9::chr16:90616204..90616205,-p@chr16:90616204..90616205
-
Mm9::chr17:3482180..3482187,+p14@Tiam2
Mm9::chr17:3482244..3482255,+p7@Tiam2
Mm9::chr18:37338354..37338370,-p3@ENSMUST00000097611
p3@uc008epl.1
Mm9::chr19:59244875..59244895,-p2@Vax1
Mm9::chr1:137499820..137499838,-p@chr1:137499820..137499838
-
Mm9::chr2:158436302..158436316,-p1@ENSMUST00000155319
Mm9::chr2:158436327..158436351,-p1@ENSMUST00000123016
Mm9::chr2:158436364..158436384,-p1@ENSMUST00000145773
Mm9::chr2:35959541..35959548,-p2@Lhx6
Mm9::chr2:35959587..35959593,-p8@Lhx6
Mm9::chr2:35960327..35960338,-p@chr2:35960327..35960338
-
Mm9::chr2:71366574..71366587,+p8@Dlx1
Mm9::chr2:71366595..71366604,+p10@Dlx1
Mm9::chr2:71366660..71366702,+p3@Dlx1
Mm9::chr2:71366714..71366725,+p12@Dlx1
Mm9::chr2:71367957..71367960,+p14@Dlx1
Mm9::chr2:71367979..71367993,+p7@Dlx1
Mm9::chr2:71368647..71368658,-p@chr2:71368647..71368658
-
Mm9::chr2:71368786..71368813,+p5@Dlx1
Mm9::chr2:71368815..71368836,+p4@Dlx1
Mm9::chr2:71375735..71375738,-p1@ENSMUST00000143767
Mm9::chr2:71375948..71375964,-p1@Dlx1as
Mm9::chr2:71381930..71381935,-p@chr2:71381930..71381935
-
Mm9::chr2:71384193..71384205,-p5@Dlx2
Mm9::chr2:71384541..71384555,-p6@Dlx2
Mm9::chr2:71384802..71384815,-p1@Dlx2
Mm9::chr2:73109983..73109996,+p1@Sp9
Mm9::chr2:73110004..73110016,+p2@Sp9
Mm9::chr2:73112323..73112364,+p@chr2:73112323..73112364
+
Mm9::chr2:73112770..73112782,+p@chr2:73112770..73112782
+
Mm9::chr2:73112788..73112806,+p@chr2:73112788..73112806
+
Mm9::chr2:73112856..73112865,+p@chr2:73112856..73112865
+
Mm9::chr3:120862141..120862150,-p3@Rwdd3
Mm9::chr4:128365970..128365994,+p5@Phc2
Mm9::chr4:45837140..45837184,+p@chr4:45837140..45837184
+
Mm9::chr5:110816192..110816193,-p8@Fbrsl1
Mm9::chr5:66728886..66728916,-p4@Apbb2
Mm9::chr5:75471615..75471622,+p1@Gsx2
Mm9::chr6:6821562..6821573,-p@chr6:6821562..6821573
-
Mm9::chr6:6821621..6821635,-p@chr6:6821621..6821635
-
Mm9::chr6:6827952..6827955,-p@chr6:6827952..6827955
-
Mm9::chr8:12323660..12323675,+p@chr8:12323660..12323675
+
Mm9::chr8:12385739..12385750,+p5@Gm5607
Mm9::chr8:12385751..12385766,+p1@Gm5607
Mm9::chr8:12385769..12385780,+p2@Gm5607
Mm9::chr8:12395287..12395295,+p9@Sox1
Mm9::chr8:12395500..12395511,+p5@Sox1
Mm9::chr8:12395603..12395621,+p1@Sox1
Mm9::chr8:12395629..12395644,+p6@Sox1
Mm9::chr8:12395670..12395682,+p3@Sox1
Mm9::chr8:47379946..47379955,-p1@Helt
Mm9::chrX:90531838..90531861,+p1@Arx


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:0005667transcription factor complex2.21598297079184e-06
GO:0044451nucleoplasm part4.71903345537537e-06
GO:0005654nucleoplasm4.71903345537537e-06
GO:0044428nuclear part8.56592444544805e-06
GO:0031981nuclear lumen9.21780987515847e-06
GO:0031974membrane-enclosed lumen1.49106954409539e-05
GO:0043233organelle lumen1.49106954409539e-05
GO:0003700transcription factor activity2.46030139664426e-05
GO:0003677DNA binding3.33490513317119e-05
GO:0030182neuron differentiation3.33490513317119e-05
GO:0048699generation of neurons5.70035228731143e-05
GO:0022008neurogenesis7.37798786953293e-05
GO:0043234protein complex9.60423051146278e-05
GO:0001764neuron migration0.000157786843389063
GO:0043565sequence-specific DNA binding0.000186253501749232
GO:0045449regulation of transcription0.000310268030717556
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.000337541542471085
GO:0006350transcription0.000350968443073521
GO:0032991macromolecular complex0.000368328280140195
GO:0010468regulation of gene expression0.000397195139001037
GO:0003676nucleic acid binding0.000397195139001037
GO:0031323regulation of cellular metabolic process0.000492393669272784
GO:0007275multicellular organismal development0.000539435425325133
GO:0003682chromatin binding0.000539435425325133
GO:0019222regulation of metabolic process0.000565341715550315
GO:0007399nervous system development0.000627396239844129
GO:0044446intracellular organelle part0.000758170481936015
GO:0005634nucleus0.000758170481936015
GO:0044422organelle part0.000758170481936015
GO:0048468cell development0.000773076278392164
GO:0048869cellular developmental process0.000785907451478338
GO:0030154cell differentiation0.000785907451478338
GO:0006355regulation of transcription, DNA-dependent0.00118462929269046
GO:0006351transcription, DNA-dependent0.0012236684118448
GO:0032774RNA biosynthetic process0.0012236684118448
GO:0010467gene expression0.00173410290397194
GO:0007420brain development0.00219247324422909
GO:0032502developmental process0.00243399745371334
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00321737793986475
GO:0048666neuron development0.00332975180353593
GO:0016070RNA metabolic process0.00356329183884163
GO:0007417central nervous system development0.0037537705428555
GO:0021889olfactory bulb interneuron differentiation0.00428091463779768
GO:0050794regulation of cellular process0.00462055366504015
GO:0043283biopolymer metabolic process0.00462055366504015
GO:0016477cell migration0.00556173952584924
GO:0043170macromolecule metabolic process0.00669180645734662
GO:0060163subpallium neuron fate commitment0.00766724058785636
GO:0007411axon guidance0.00797039814144068
GO:0006928cell motility0.00820820407149906
GO:0051674localization of cell0.00820820407149906
GO:0050789regulation of biological process0.0082387232507014
GO:0021988olfactory lobe development0.00985437040322196
GO:0045749negative regulation of S phase of mitotic cell cycle0.00985437040322196
GO:0021772olfactory bulb development0.00985437040322196
GO:0035035histone acetyltransferase binding0.00985437040322196
GO:0030900forebrain development0.0109073978209299
GO:0006357regulation of transcription from RNA polymerase II promoter0.011367274065383
GO:0048523negative regulation of cellular process0.0113689806791655
GO:0021798forebrain dorsal/ventral pattern formation0.0122588499778052
GO:0065007biological regulation0.0131298057511698
GO:0048519negative regulation of biological process0.0131298057511698
GO:0006366transcription from RNA polymerase II promoter0.0131298057511698
GO:0021884forebrain neuron development0.0131298057511698
GO:0033261regulation of progression through S phase0.0131298057511698
GO:0045930negative regulation of progression through mitotic cell cycle0.0131298057511698
GO:0021544subpallium development0.0131298057511698
GO:0007090regulation of S phase of mitotic cell cycle0.0131298057511698
GO:0031490chromatin DNA binding0.0131298057511698
GO:0048665neuron fate specification0.0131298057511698
GO:0032501multicellular organismal process0.0137681597575249
GO:0021871forebrain regionalization0.0151028909639773
GO:0007406negative regulation of neuroblast proliferation0.0151028909639773
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0162281337282585
GO:0051320S phase0.0164846794619366
GO:0001540beta-amyloid binding0.0164846794619366
GO:0021879forebrain neuron differentiation0.0164846794619366
GO:0000084S phase of mitotic cell cycle0.0164846794619366
GO:0043066negative regulation of apoptosis0.0171580623244607
GO:0048731system development0.0171731729320548
GO:0043069negative regulation of programmed cell death0.0171731729320548
GO:0007409axonogenesis0.0172819807236409
GO:0050821protein stabilization0.0172819807236409
GO:0008641small protein activating enzyme activity0.0172819807236409
GO:0021872generation of neurons in the forebrain0.0172819807236409
GO:0048667neuron morphogenesis during differentiation0.0185426164403585
GO:0048812neurite morphogenesis0.0185426164403585
GO:0031647regulation of protein stability0.0187727410988563
GO:0044238primary metabolic process0.0201624510986748
GO:0044237cellular metabolic process0.0201624510986748
GO:0043231intracellular membrane-bound organelle0.0201624510986748
GO:0043227membrane-bound organelle0.0201624510986748
GO:0031519PcG protein complex0.0216954381239689
GO:0000904cellular morphogenesis during differentiation0.0219034661513601
GO:0008134transcription factor binding0.0219034661513601
GO:0045892negative regulation of transcription, DNA-dependent0.0219034661513601
GO:0003727single-stranded RNA binding0.0226836865020366
GO:0031175neurite development0.0232552390551862
GO:0030308negative regulation of cell growth0.0240689825316621
GO:0048856anatomical structure development0.0263546774688718
GO:0030048actin filament-based movement0.0272025987851738
GO:0016481negative regulation of transcription0.0326944859935074
GO:0045792negative regulation of cell size0.0337395210907081
GO:0050768negative regulation of neurogenesis0.0348264151480951
GO:0007346regulation of progression through mitotic cell cycle0.0348264151480951
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0355393243255663
GO:0048663neuron fate commitment0.0355393243255663
GO:0021954central nervous system neuron development0.0355393243255663
GO:0032990cell part morphogenesis0.0368491736529409
GO:0048858cell projection morphogenesis0.0368491736529409
GO:0030030cell projection organization and biogenesis0.0368491736529409
GO:0001708cell fate specification0.0368491736529409
GO:0043524negative regulation of neuron apoptosis0.0368491736529409
GO:0021537telencephalon development0.0368491736529409
GO:0021953central nervous system neuron differentiation0.0381034026033847
GO:0045926negative regulation of growth0.0393348936321501
GO:0007405neuroblast proliferation0.0405442304895145
GO:0031324negative regulation of cellular metabolic process0.0415817369426005
GO:0043229intracellular organelle0.0481335951924562
GO:0043226organelle0.0481335951924562
GO:0016874ligase activity0.0489674259356976



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
neuron of cerebral cortex9.89e-126
CNS neuron (sensu Vertebrata)1.76e-0723
neuroblast (sensu Vertebrata)1.76e-0723
hippocampal neuron6.23e-073

Uber Anatomy
Ontology termp-valuen
regional part of forebrain5.62e-1539
forebrain5.62e-1539
future forebrain5.62e-1539
brain1.80e-1447
future brain1.80e-1447
anterior neural tube1.88e-1440
regional part of brain2.71e-1346
pre-chordal neural plate5.22e-1349
brain grey matter2.10e-1229
regional part of telencephalon2.10e-1229
telencephalon2.10e-1229
regional part of nervous system1.72e-1154
neural tube4.68e-1152
neural rod4.68e-1152
future spinal cord4.68e-1152
neural keel4.68e-1152
gray matter6.18e-1034
corpus striatum7.56e-105
striatum7.56e-105
ventral part of telencephalon7.56e-105
future corpus striatum7.56e-105
neurectoderm1.33e-0964
neural plate1.33e-0964
presumptive neural plate1.33e-0964
central nervous system7.15e-0873
basal ganglion7.36e-088
nuclear complex of neuraxis7.36e-088
aggregate regional part of brain7.36e-088
collection of basal ganglia7.36e-088
cerebral subcortex7.36e-088
ecto-epithelium1.18e-0773
nervous system1.69e-0775
Ammon's horn7.27e-077
lobe parts of cerebral cortex7.27e-077
hippocampal formation7.27e-077
limbic system7.27e-077
limbic lobe7.27e-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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