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MCL coexpression mm9:1831: Difference between revisions

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{{MCL_coexpression_mm9
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limb morphogenesis;0.000258943501150261;13396,13395!GO:0035113;embryonic appendage morphogenesis;0.000258943501150261;13396,13395!GO:0035107;appendage morphogenesis;0.000258943501150261;13396,13395!GO:0035108;limb morphogenesis;0.000258943501150261;13396,13395!GO:0048736;appendage development;0.000258943501150261;13396,13395!GO:0060173;limb development;0.000258943501150261;13396,13395!GO:0048598;embryonic morphogenesis;0.0014479800732008;13396,13395!GO:0005667;transcription factor complex;0.00502663040665224;13396,13395!GO:0043565;sequence-specific DNA binding;0.00502663040665224;13396,13395!GO:0009790;embryonic development;0.00502663040665224;13396,13395!GO:0044451;nucleoplasm part;0.0062098763682065;13396,13395!GO:0005654;nucleoplasm;0.00625233833473574;13396,13395!GO:0031981;nuclear lumen;0.00815663300844468;13396,13395!GO:0031974;membrane-enclosed lumen;0.00899439116634181;13396,13395!GO:0043233;organelle lumen;0.00899439116634181;13396,13395!GO:0003700;transcription factor activity;0.0101738699893271;13396,13395!GO:0044428;nuclear part;0.0140269986754033;13396,13395!GO:0009653;anatomical structure morphogenesis;0.0172120806986589;13396,13395!GO:0042472;inner ear morphogenesis;0.0261206619311803;13395!GO:0042471;ear morphogenesis;0.0275672713712403;13395!GO:0043234;protein complex;0.0291253627649331;13396,13395!GO:0048839;inner ear development;0.0292299925869118;13395!GO:0043583;ear development;0.0303461707032352;13395!GO:0006355;regulation of transcription, DNA-dependent;0.0303461707032352;13396,13395!GO:0006351;transcription, DNA-dependent;0.0303461707032352;13396,13395!GO:0032774;RNA biosynthetic process;0.0303461707032352;13396,13395!GO:0003677;DNA binding;0.0303461707032352;13396,13395!GO:0045449;regulation of transcription;0.0303461707032352;13396,13395!GO:0048856;anatomical structure development;0.0303461707032352;13396,13395!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0303461707032352;13396,13395!GO:0006350;transcription;0.0303461707032352;13396,13395!GO:0032991;macromolecular complex;0.0303461707032352;13396,13395!GO:0010468;regulation of gene expression;0.0305772001889394;13396,13395!GO:0031323;regulation of cellular metabolic process;0.0321607116515682;13396,13395!GO:0007275;multicellular organismal development;0.0326616758899756;13396,13395!GO:0019222;regulation of metabolic process;0.0326616758899756;13396,13395!GO:0016070;RNA metabolic process;0.0334786777647593;13396,13395!GO:0044446;intracellular organelle part;0.0340365919858891;13396,13395!GO:0044422;organelle part;0.0340365919858891;13396,13395!GO:0007409;axonogenesis;0.0352867503015634;13395!GO:0048667;neuron morphogenesis during differentiation;0.0355616341903106;13395!GO:0048812;neurite morphogenesis;0.0355616341903106;13395!GO:0000904;cellular morphogenesis during differentiation;0.0387104947640834;13395!GO:0007423;sensory organ development;0.0387104947640834;13395!GO:0010467;gene expression;0.0388094600719565;13396,13395!GO:0031175;neurite development;0.0388094600719565;13395!GO:0003676;nucleic acid binding;0.0395873215100833;13396,13395!GO:0032502;developmental process;0.0407048398569286;13396,13395!GO:0048666;neuron development;0.0407048398569286;13395!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0432173728216949;13396,13395!GO:0032990;cell part morphogenesis;0.0460040440688511;13395!GO:0030030;cell projection organization and biogenesis;0.0460040440688511;13395!GO:0048858;cell projection morphogenesis;0.0460040440688511;13395!GO:0050794;regulation of cellular process;0.0460040440688511;13396,13395!GO:0030182;neuron 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|gostat_on_MCL_coexpression=GO:0030326;embryonic limb morphogenesis;0.000258943501150261;13396,13395!GO:0035113;embryonic appendage morphogenesis;0.000258943501150261;13396,13395!GO:0035107;appendage morphogenesis;0.000258943501150261;13396,13395!GO:0035108;limb morphogenesis;0.000258943501150261;13396,13395!GO:0048736;appendage development;0.000258943501150261;13396,13395!GO:0060173;limb development;0.000258943501150261;13396,13395!GO:0048598;embryonic morphogenesis;0.0014479800732008;13396,13395!GO:0005667;transcription factor complex;0.00502663040665224;13396,13395!GO:0043565;sequence-specific DNA binding;0.00502663040665224;13396,13395!GO:0009790;embryonic development;0.00502663040665224;13396,13395!GO:0044451;nucleoplasm part;0.0062098763682065;13396,13395!GO:0005654;nucleoplasm;0.00625233833473574;13396,13395!GO:0031981;nuclear lumen;0.00815663300844468;13396,13395!GO:0031974;membrane-enclosed lumen;0.00899439116634181;13396,13395!GO:0043233;organelle lumen;0.00899439116634181;13396,13395!GO:0003700;transcription factor activity;0.0101738699893271;13396,13395!GO:0044428;nuclear part;0.0140269986754033;13396,13395!GO:0009653;anatomical structure morphogenesis;0.0172120806986589;13396,13395!GO:0042472;inner ear morphogenesis;0.0261206619311803;13395!GO:0042471;ear morphogenesis;0.0275672713712403;13395!GO:0043234;protein complex;0.0291253627649331;13396,13395!GO:0048839;inner ear development;0.0292299925869118;13395!GO:0043583;ear development;0.0303461707032352;13395!GO:0006355;regulation of transcription, DNA-dependent;0.0303461707032352;13396,13395!GO:0006351;transcription, DNA-dependent;0.0303461707032352;13396,13395!GO:0032774;RNA biosynthetic process;0.0303461707032352;13396,13395!GO:0003677;DNA binding;0.0303461707032352;13396,13395!GO:0045449;regulation of transcription;0.0303461707032352;13396,13395!GO:0048856;anatomical structure development;0.0303461707032352;13396,13395!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0303461707032352;13396,13395!GO:0006350;transcription;0.0303461707032352;13396,13395!GO:0032991;macromolecular complex;0.0303461707032352;13396,13395!GO:0010468;regulation of gene expression;0.0305772001889394;13396,13395!GO:0031323;regulation of cellular metabolic process;0.0321607116515682;13396,13395!GO:0007275;multicellular organismal development;0.0326616758899756;13396,13395!GO:0019222;regulation of metabolic process;0.0326616758899756;13396,13395!GO:0016070;RNA metabolic process;0.0334786777647593;13396,13395!GO:0044446;intracellular organelle part;0.0340365919858891;13396,13395!GO:0044422;organelle part;0.0340365919858891;13396,13395!GO:0007409;axonogenesis;0.0352867503015634;13395!GO:0048667;neuron morphogenesis during differentiation;0.0355616341903106;13395!GO:0048812;neurite morphogenesis;0.0355616341903106;13395!GO:0000904;cellular morphogenesis during differentiation;0.0387104947640834;13395!GO:0007423;sensory organ development;0.0387104947640834;13395!GO:0010467;gene expression;0.0388094600719565;13396,13395!GO:0031175;neurite development;0.0388094600719565;13395!GO:0003676;nucleic acid binding;0.0395873215100833;13396,13395!GO:0032502;developmental process;0.0407048398569286;13396,13395!GO:0048666;neuron development;0.0407048398569286;13395!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0432173728216949;13396,13395!GO:0032990;cell part morphogenesis;0.0460040440688511;13395!GO:0030030;cell projection organization and biogenesis;0.0460040440688511;13395!GO:0048858;cell projection morphogenesis;0.0460040440688511;13395!GO:0050794;regulation of cellular process;0.0460040440688511;13396,13395!GO:0030182;neuron differentiation;0.0460040440688511;13395!
}}

Latest revision as of 17:34, 17 September 2013


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)
MA0003.10.211284
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.418772
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.0851423
MA0056.10
MA0057.12.39011
MA0058.10.50032
MA0059.10.513699
MA0060.12.4023
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.11.71065
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.189951
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.148348
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.13.55698
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.295945
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.476962
MA0146.10.0604336
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.20.0511423
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.157681
MA0065.20.477991
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.11.11105
MA0155.12.24718
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.245828
MA0163.10.855539
MA0164.10.729558
MA0080.20.455167
MA0018.22.93398
MA0099.20.854449
MA0079.23.38617
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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