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MCL coexpression mm9:1095: Difference between revisions

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{{MCL_coexpression_mm9
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specification process;0.00704628605978155;15399,15413!GO:0048703;embryonic viscerocranium morphogenesis;0.00704628605978155;15399!GO:0005667;transcription factor complex;0.00704628605978155;15399,15413!GO:0043565;sequence-specific DNA binding;0.00704628605978155;15399,15413!GO:0048701;embryonic cranial skeleton morphogenesis;0.00704628605978155;15399!GO:0042474;middle ear morphogenesis;0.00704628605978155;15399!GO:0009887;organ morphogenesis;0.00704628605978155;15399,15413!GO:0044451;nucleoplasm part;0.00704628605978155;15399,15413!GO:0005654;nucleoplasm;0.00704628605978155;15399,15413!GO:0045446;endothelial cell differentiation;0.00746882169324845;15413!GO:0048704;embryonic skeletal morphogenesis;0.00746882169324845;15399!GO:0031981;nuclear lumen;0.00746882169324845;15399,15413!GO:0031974;membrane-enclosed lumen;0.00814543077564118;15399,15413!GO:0043233;organelle lumen;0.00814543077564118;15399,15413!GO:0048706;embryonic skeletal development;0.00829476945773949;15399!GO:0003700;transcription factor activity;0.00859934249097884;15399,15413!GO:0048705;skeletal morphogenesis;0.0103661885975155;15399!GO:0001709;cell fate determination;0.0103661885975155;15399!GO:0044428;nuclear part;0.010608137469431;15399,15413!GO:0009653;anatomical structure morphogenesis;0.013093475674337;15399,15413!GO:0048513;organ development;0.0177494802129741;15399,15413!GO:0042471;ear morphogenesis;0.0211826435861262;15399!GO:0043234;protein complex;0.0221767273126586;15399,15413!GO:0048731;system development;0.0221767273126586;15399,15413!GO:0043583;ear development;0.0221767273126586;15399!GO:0048869;cellular developmental process;0.0221767273126586;15399,15413!GO:0030154;cell differentiation;0.0221767273126586;15399,15413!GO:0006355;regulation of transcription, DNA-dependent;0.0221767273126586;15399,15413!GO:0006351;transcription, DNA-dependent;0.0221767273126586;15399,15413!GO:0032774;RNA biosynthetic process;0.0221767273126586;15399,15413!GO:0003677;DNA binding;0.0221767273126586;15399,15413!GO:0045449;regulation of transcription;0.0221767273126586;15399,15413!GO:0048856;anatomical structure development;0.0221767273126586;15399,15413!GO:0045165;cell fate commitment;0.0221767273126586;15399!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0221767273126586;15399,15413!GO:0006350;transcription;0.0221767273126586;15399,15413!GO:0032991;macromolecular complex;0.0221835585063547;15399,15413!GO:0010468;regulation of gene expression;0.022444354649964;15399,15413!GO:0031323;regulation of cellular metabolic process;0.0236983998555817;15399,15413!GO:0007275;multicellular organismal development;0.0241833631015704;15399,15413!GO:0019222;regulation of metabolic process;0.0242401984828042;15399,15413!GO:0016070;RNA metabolic process;0.0249287093220019;15399,15413!GO:0044446;intracellular organelle part;0.0254998168855322;15399,15413!GO:0044422;organelle part;0.0254998168855322;15399,15413!GO:0001501;skeletal development;0.0309655821500028;15399!GO:0007423;sensory organ development;0.031296994214026;15399!GO:0010467;gene expression;0.031902634374277;15399,15413!GO:0048598;embryonic morphogenesis;0.0320949688724849;15399!GO:0003676;nucleic acid binding;0.0320949688724849;15399,15413!GO:0032502;developmental process;0.0333071565541416;15399,15413!GO:0043009;chordate embryonic development;0.0333071565541416;15399!GO:0009792;embryonic development ending in birth or egg hatching;0.0333071565541416;15399!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0344612923443434;15399,15413!GO:0050794;regulation of cellular process;0.0388992151408601;15399,15413!GO:0050789;regulation of biological 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|gostat_on_MCL_coexpression=GO:0007389;pattern specification process;0.00704628605978155;15399,15413!GO:0048703;embryonic viscerocranium morphogenesis;0.00704628605978155;15399!GO:0005667;transcription factor complex;0.00704628605978155;15399,15413!GO:0043565;sequence-specific DNA binding;0.00704628605978155;15399,15413!GO:0048701;embryonic cranial skeleton morphogenesis;0.00704628605978155;15399!GO:0042474;middle ear morphogenesis;0.00704628605978155;15399!GO:0009887;organ morphogenesis;0.00704628605978155;15399,15413!GO:0044451;nucleoplasm part;0.00704628605978155;15399,15413!GO:0005654;nucleoplasm;0.00704628605978155;15399,15413!GO:0045446;endothelial cell differentiation;0.00746882169324845;15413!GO:0048704;embryonic skeletal morphogenesis;0.00746882169324845;15399!GO:0031981;nuclear lumen;0.00746882169324845;15399,15413!GO:0031974;membrane-enclosed lumen;0.00814543077564118;15399,15413!GO:0043233;organelle lumen;0.00814543077564118;15399,15413!GO:0048706;embryonic skeletal development;0.00829476945773949;15399!GO:0003700;transcription factor activity;0.00859934249097884;15399,15413!GO:0048705;skeletal morphogenesis;0.0103661885975155;15399!GO:0001709;cell fate determination;0.0103661885975155;15399!GO:0044428;nuclear part;0.010608137469431;15399,15413!GO:0009653;anatomical structure morphogenesis;0.013093475674337;15399,15413!GO:0048513;organ development;0.0177494802129741;15399,15413!GO:0042471;ear morphogenesis;0.0211826435861262;15399!GO:0043234;protein complex;0.0221767273126586;15399,15413!GO:0048731;system development;0.0221767273126586;15399,15413!GO:0043583;ear development;0.0221767273126586;15399!GO:0048869;cellular developmental process;0.0221767273126586;15399,15413!GO:0030154;cell differentiation;0.0221767273126586;15399,15413!GO:0006355;regulation of transcription, DNA-dependent;0.0221767273126586;15399,15413!GO:0006351;transcription, DNA-dependent;0.0221767273126586;15399,15413!GO:0032774;RNA biosynthetic process;0.0221767273126586;15399,15413!GO:0003677;DNA binding;0.0221767273126586;15399,15413!GO:0045449;regulation of transcription;0.0221767273126586;15399,15413!GO:0048856;anatomical structure development;0.0221767273126586;15399,15413!GO:0045165;cell fate commitment;0.0221767273126586;15399!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0221767273126586;15399,15413!GO:0006350;transcription;0.0221767273126586;15399,15413!GO:0032991;macromolecular complex;0.0221835585063547;15399,15413!GO:0010468;regulation of gene expression;0.022444354649964;15399,15413!GO:0031323;regulation of cellular metabolic process;0.0236983998555817;15399,15413!GO:0007275;multicellular organismal development;0.0241833631015704;15399,15413!GO:0019222;regulation of metabolic process;0.0242401984828042;15399,15413!GO:0016070;RNA metabolic process;0.0249287093220019;15399,15413!GO:0044446;intracellular organelle part;0.0254998168855322;15399,15413!GO:0044422;organelle part;0.0254998168855322;15399,15413!GO:0001501;skeletal development;0.0309655821500028;15399!GO:0007423;sensory organ development;0.031296994214026;15399!GO:0010467;gene expression;0.031902634374277;15399,15413!GO:0048598;embryonic morphogenesis;0.0320949688724849;15399!GO:0003676;nucleic acid binding;0.0320949688724849;15399,15413!GO:0032502;developmental process;0.0333071565541416;15399,15413!GO:0043009;chordate embryonic development;0.0333071565541416;15399!GO:0009792;embryonic development ending in birth or egg hatching;0.0333071565541416;15399!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0344612923443434;15399,15413!GO:0050794;regulation of cellular process;0.0388992151408601;15399,15413!GO:0050789;regulation of biological process;0.0473715943392161;15399,15413!
}}

Latest revision as of 16:23, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:96164887..96164894,+p4@Hoxb5
Mm9::chr11:96164905..96164919,+p2@Hoxb5
Mm9::chr11:96164928..96164947,+p@chr11:96164928..96164947
+
Mm9::chr11:96164964..96165032,+p@chr11:96164964..96165032
+
Mm9::chr11:96165039..96165073,+p@chr11:96165039..96165073
+
Mm9::chr6:52114447..52114463,-p@chr6:52114447..52114463
-
Mm9::chr6:52114472..52114489,-p@chr6:52114472..52114489
-


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:0007389pattern specification process0.00704628605978155
GO:0048703embryonic viscerocranium morphogenesis0.00704628605978155
GO:0005667transcription factor complex0.00704628605978155
GO:0043565sequence-specific DNA binding0.00704628605978155
GO:0048701embryonic cranial skeleton morphogenesis0.00704628605978155
GO:0042474middle ear morphogenesis0.00704628605978155
GO:0009887organ morphogenesis0.00704628605978155
GO:0044451nucleoplasm part0.00704628605978155
GO:0005654nucleoplasm0.00704628605978155
GO:0045446endothelial cell differentiation0.00746882169324845
GO:0048704embryonic skeletal morphogenesis0.00746882169324845
GO:0031981nuclear lumen0.00746882169324845
GO:0031974membrane-enclosed lumen0.00814543077564118
GO:0043233organelle lumen0.00814543077564118
GO:0048706embryonic skeletal development0.00829476945773949
GO:0003700transcription factor activity0.00859934249097884
GO:0048705skeletal morphogenesis0.0103661885975155
GO:0001709cell fate determination0.0103661885975155
GO:0044428nuclear part0.010608137469431
GO:0009653anatomical structure morphogenesis0.013093475674337
GO:0048513organ development0.0177494802129741
GO:0042471ear morphogenesis0.0211826435861262
GO:0043234protein complex0.0221767273126586
GO:0048731system development0.0221767273126586
GO:0043583ear development0.0221767273126586
GO:0048869cellular developmental process0.0221767273126586
GO:0030154cell differentiation0.0221767273126586
GO:0006355regulation of transcription, DNA-dependent0.0221767273126586
GO:0006351transcription, DNA-dependent0.0221767273126586
GO:0032774RNA biosynthetic process0.0221767273126586
GO:0003677DNA binding0.0221767273126586
GO:0045449regulation of transcription0.0221767273126586
GO:0048856anatomical structure development0.0221767273126586
GO:0045165cell fate commitment0.0221767273126586
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0221767273126586
GO:0006350transcription0.0221767273126586
GO:0032991macromolecular complex0.0221835585063547
GO:0010468regulation of gene expression0.022444354649964
GO:0031323regulation of cellular metabolic process0.0236983998555817
GO:0007275multicellular organismal development0.0241833631015704
GO:0019222regulation of metabolic process0.0242401984828042
GO:0016070RNA metabolic process0.0249287093220019
GO:0044446intracellular organelle part0.0254998168855322
GO:0044422organelle part0.0254998168855322
GO:0001501skeletal development0.0309655821500028
GO:0007423sensory organ development0.031296994214026
GO:0010467gene expression0.031902634374277
GO:0048598embryonic morphogenesis0.0320949688724849
GO:0003676nucleic acid binding0.0320949688724849
GO:0032502developmental process0.0333071565541416
GO:0043009chordate embryonic development0.0333071565541416
GO:0009792embryonic development ending in birth or egg hatching0.0333071565541416
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0344612923443434
GO:0050794regulation of cellular process0.0388992151408601
GO:0050789regulation of biological process0.0473715943392161



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
lung6.83e-1214
respiratory tube6.83e-1214
respiration organ6.83e-1214
pair of lungs6.83e-1214
lung primordium6.83e-1214
lung bud6.83e-1214
epithelial fold1.70e-1120
thoracic cavity element7.83e-1017
thoracic segment organ7.83e-1017
thoracic cavity7.83e-1017
thoracic segment of trunk7.83e-1017
respiratory primordium7.83e-1017
endoderm of foregut7.83e-1017
epithelial bud8.23e-0917


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)
MA0003.10.188259
MA0004.13.10641
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.10.0200028
MA0017.11.60852
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.0406078
MA0056.10
MA0057.11.23731
MA0058.14.70026
MA0059.12.71878
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.771749
MA0069.10.945354
MA0070.12.15469
MA0071.10.519509
MA0072.10.927016
MA0073.11.85276
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.112.6395
MA0084.11.59945
MA0087.10.977537
MA0088.10.0841779
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.12.39775
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.719313
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.631666
MA0146.10.108739
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.00226251
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.218974
MA0047.20.626803
MA0112.20.0910939
MA0065.20.305574
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.10.102995
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.55478
MA0163.10.82914
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.105858
MA0102.21.65195
MA0258.10.246285
MA0259.10.729797
MA0442.10
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