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MCL coexpression mm9:212: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.202843190349958,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.433594786201484,0.323116468687679,0,0,0,1.11769367894131,1.17740971907324,1.23760135185748,0,0,0,0.901979759657372,0.641134440747991,1.11120413298,0.486061930039393,0.330205393193943,0,0.184715090233432,0.313445759032225,0,0,0,0,0,0,0.0570741246689917,0,0,0,0.0572260417947564,0,0,0,0,0,0,0.0469568706916304,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.484223735611534,0.732263519756413,0,0,0,0,0.662283185526628,0.709058311755839,0,0.408988965919217,0.706841254353106,0.777202952192588,1.06241959539583,0,0,0,0.0829439327499637,0,0,0,0,0,0,0,0.554735457764554,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.491767707411952,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.870522330923759,1.25516861319845,0,0,0.119093565942036,0,0.317460957825606,0.0930603692915911,0.325103621004514,0.108252561213616,0.1476178069765,0.199895454695966,0.252992651410535,0.358940419539848,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.14550006174377,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0677982110636083,0.0481920468563092,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.12789943065388,0.92247652524325,0.981974033303001,0.824201032451998,0.708462977800011,0.798495768839123,0.703302987935577,0.568427876181492,0.570409181558021,0.613478370404309,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0905641158318875
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.202843190349958,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.433594786201484,0.323116468687679,0,0,0,1.11769367894131,1.17740971907324,1.23760135185748,0,0,0,0.901979759657372,0.641134440747991,1.11120413298,0.486061930039393,0.330205393193943,0,0.184715090233432,0.313445759032225,0,0,0,0,0,0,0.0570741246689917,0,0,0,0.0572260417947564,0,0,0,0,0,0,0.0469568706916304,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.484223735611534,0.732263519756413,0,0,0,0,0.662283185526628,0.709058311755839,0,0.408988965919217,0.706841254353106,0.777202952192588,1.06241959539583,0,0,0,0.0829439327499637,0,0,0,0,0,0,0,0.554735457764554,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.491767707411952,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.870522330923759,1.25516861319845,0,0,0.119093565942036,0,0.317460957825606,0.0930603692915911,0.325103621004514,0.108252561213616,0.1476178069765,0.199895454695966,0.252992651410535,0.358940419539848,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.14550006174377,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0677982110636083,0.0481920468563092,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.12789943065388,0.92247652524325,0.981974033303001,0.824201032451998,0.708462977800011,0.798495768839123,0.703302987935577,0.568427876181492,0.570409181558021,0.613478370404309,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0905641158318875
|gostat_on_MCL_coexpression=GO:0022010;myelination in the central nervous system;0.00345148742672438;18823!GO:0032291;ensheathment of axons in the central nervous system;0.00345148742672438;18823!GO:0004308;exo-alpha-sialidase activity;0.00460185716771568;241159!GO:0016997;alpha-sialidase activity;0.00493015603281988;241159!GO:0042759;long-chain fatty acid biosynthetic process;0.00493015603281988;18823!GO:0043209;myelin sheath;0.00493015603281988;18823!GO:0014003;oligodendrocyte development;0.00493015603281988;18823!GO:0021782;glial cell development;0.00766808104063517;18823!GO:0048709;oligodendrocyte differentiation;0.00766808104063517;18823!GO:0001676;long-chain fatty acid metabolic process;0.00966072314069902;18823!GO:0042552;myelination;0.0153871323097943;18823!GO:0008366;axon ensheathment;0.0153871323097943;18823!GO:0007272;ensheathment of neurons;0.0153871323097943;18823!GO:0001508;regulation of action potential;0.0174698111462984;18823!GO:0010001;glial cell differentiation;0.0174698111462984;18823!GO:0042063;gliogenesis;0.0176694901197512;18823!GO:0006633;fatty acid biosynthetic process;0.0254899305412603;18823!GO:0046394;carboxylic acid biosynthetic process;0.0254899305412603;18823!GO:0016053;organic acid biosynthetic process;0.0254899305412603;18823!GO:0048469;cell maturation;0.0254899305412603;18823!GO:0004553;hydrolase activity, hydrolyzing O-glycosyl compounds;0.0284828166957132;241159!GO:0021700;developmental maturation;0.0284828166957132;18823!GO:0016798;hydrolase activity, acting on glycosyl bonds;0.0323189575174909;241159!GO:0006631;fatty acid metabolic process;0.0458193843685796;18823!
|gostat_on_MCL_coexpression=GO:0022010;myelination in the central nervous system;0.00345148742672438;18823!GO:0032291;ensheathment of axons in the central nervous system;0.00345148742672438;18823!GO:0004308;exo-alpha-sialidase activity;0.00460185716771568;241159!GO:0016997;alpha-sialidase activity;0.00493015603281988;241159!GO:0042759;long-chain fatty acid biosynthetic process;0.00493015603281988;18823!GO:0043209;myelin sheath;0.00493015603281988;18823!GO:0014003;oligodendrocyte development;0.00493015603281988;18823!GO:0021782;glial cell development;0.00766808104063517;18823!GO:0048709;oligodendrocyte differentiation;0.00766808104063517;18823!GO:0001676;long-chain fatty acid metabolic process;0.00966072314069902;18823!GO:0042552;myelination;0.0153871323097943;18823!GO:0008366;axon ensheathment;0.0153871323097943;18823!GO:0007272;ensheathment of neurons;0.0153871323097943;18823!GO:0001508;regulation of action potential;0.0174698111462984;18823!GO:0010001;glial cell differentiation;0.0174698111462984;18823!GO:0042063;gliogenesis;0.0176694901197512;18823!GO:0006633;fatty acid biosynthetic process;0.0254899305412603;18823!GO:0046394;carboxylic acid biosynthetic process;0.0254899305412603;18823!GO:0016053;organic acid biosynthetic process;0.0254899305412603;18823!GO:0048469;cell maturation;0.0254899305412603;18823!GO:0004553;hydrolase activity, hydrolyzing O-glycosyl compounds;0.0284828166957132;241159!GO:0021700;developmental maturation;0.0284828166957132;18823!GO:0016798;hydrolase activity, acting on glycosyl bonds;0.0323189575174909;241159!GO:0006631;fatty acid metabolic process;0.0458193843685796;18823!
|ontology_enrichment_celltype=CL:0000540!3.74e-13!33;CL:0000047!3.74e-13!33;CL:0000031!3.74e-13!33;CL:0000404!3.74e-13!33;CL:0000221!2.43e-12!44;CL:0000133!2.43e-12!44;CL:0002319!1.74e-11!43;CL:0000393!1.97e-10!39;CL:0000211!1.97e-10!39;CL:0000107!4.02e-10!9;CL:0000055!1.80e-09!49;CL:0002610!2.89e-07!3
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!3.08e-35!75;UBERON:0001017!1.08e-32!73;UBERON:0004121!3.30e-30!95;UBERON:0000924!3.30e-30!95;UBERON:0006601!3.30e-30!95;UBERON:0000073!1.42e-25!54;UBERON:0002346!8.13e-23!64;UBERON:0003075!8.13e-23!64;UBERON:0007284!8.13e-23!64;UBERON:0001049!1.58e-22!52;UBERON:0005068!1.58e-22!52;UBERON:0006241!1.58e-22!52;UBERON:0007135!1.58e-22!52;UBERON:0010371!2.86e-20!73;UBERON:0002021!3.46e-18!10;UBERON:0000411!3.46e-18!10;UBERON:0001950!3.46e-18!10;UBERON:0000955!4.40e-18!47;UBERON:0006238!4.40e-18!47;UBERON:0002020!1.35e-17!34;UBERON:0002616!5.96e-17!46;UBERON:0010314!2.73e-14!92;UBERON:0003528!1.76e-13!29;UBERON:0002791!1.76e-13!29;UBERON:0001893!1.76e-13!29;UBERON:0003080!5.20e-13!40;UBERON:0000010!1.22e-12!11;UBERON:0003056!4.18e-12!49;UBERON:0002780!6.72e-12!39;UBERON:0001890!6.72e-12!39;UBERON:0006240!6.72e-12!39;UBERON:0002619!9.41e-12!17;UBERON:0003076!2.63e-11!12;UBERON:0003057!2.63e-11!12;UBERON:0000956!9.80e-11!21;UBERON:0001869!9.80e-11!21;UBERON:0000203!9.80e-11!21;UBERON:0002410!4.02e-10!9;UBERON:0002950!2.82e-08!4;UBERON:0001891!2.82e-08!4;UBERON:0009616!2.82e-08!4;UBERON:0010286!2.82e-08!4;UBERON:0011216!6.69e-08!194;UBERON:0002240!2.05e-07!6;UBERON:0005174!2.05e-07!6;UBERON:0001137!2.05e-07!6;UBERON:0004684!2.89e-07!3;UBERON:0002275!2.89e-07!3
}}
}}

Revision as of 17:57, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:86484671..86484688,-p14@Vmp1
Mm9::chr1:95917036..95917062,+p1@Neu4
Mm9::chr4:101223802..101223807,-p@chr4:101223802..101223807
-
Mm9::chr9:120084007..120084018,+p@chr9:120084007..120084018
+
Mm9::chr9:120084080..120084094,+p@chr9:120084080..120084094
+
Mm9::chr9:120084144..120084162,+p@chr9:120084144..120084162
+
Mm9::chr9:120088783..120088795,+p@chr9:120088783..120088795
+
Mm9::chr9:120089157..120089170,+p@chr9:120089157..120089170
+
Mm9::chr9:120089403..120089416,+p@chr9:120089403..120089416
+
Mm9::chrX:133365683..133365695,+p12@Plp1
Mm9::chrX:133365756..133365765,+p14@Plp1
Mm9::chrX:133366557..133366580,+p@chrX:133366557..133366580
+
Mm9::chrX:133366664..133366688,+p@chrX:133366664..133366688
+
Mm9::chrX:133367808..133367821,+p4@Plp1
Mm9::chrX:133367835..133367892,+p3@Plp1
Mm9::chrX:133367942..133367952,+p10@Plp1
Mm9::chrX:133368690..133368741,+p@chrX:133368690..133368741
+
Mm9::chrX:133369636..133369682,+p@chrX:133369636..133369682
+
Mm9::chrX:133371343..133371355,+p@chrX:133371343..133371355
+
Mm9::chrX:133371663..133371686,+p@chrX:133371663..133371686
+
Mm9::chrX:133371693..133371705,+p@chrX:133371693..133371705
+
Mm9::chrX:133371747..133371758,+p@chrX:133371747..133371758
+
Mm9::chrX:133371769..133371785,+p@chrX:133371769..133371785
+
Mm9::chrX:133371820..133371834,+p@chrX:133371820..133371834
+
Mm9::chrX:133371872..133371900,+p@chrX:133371872..133371900
+
Mm9::chrX:133371908..133371920,+p@chrX:133371908..133371920
+
Mm9::chrX:133371961..133371972,+p@chrX:133371961..133371972
+
Mm9::chrX:133371982..133371996,+p@chrX:133371982..133371996
+
Mm9::chrX:133372000..133372007,+p@chrX:133372000..133372007
+
Mm9::chrX:133372008..133372027,+p@chrX:133372008..133372027
+
Mm9::chrX:133372040..133372053,+p@chrX:133372040..133372053
+
Mm9::chrX:133372057..133372068,+p@chrX:133372057..133372068
+
Mm9::chrX:133372076..133372105,+p@chrX:133372076..133372105
+
Mm9::chrX:133372108..133372115,+p@chrX:133372108..133372115
+
Mm9::chrX:133372121..133372126,+p@chrX:133372121..133372126
+
Mm9::chrX:133372129..133372164,+p@chrX:133372129..133372164
+
Mm9::chrX:133372165..133372186,+p@chrX:133372165..133372186
+
Mm9::chrX:133372407..133372423,+p@chrX:133372407..133372423
+
Mm9::chrX:133372446..133372459,+p@chrX:133372446..133372459
+
Mm9::chrX:133372528..133372539,+p@chrX:133372528..133372539
+
Mm9::chrX:133372559..133372564,+p@chrX:133372559..133372564
+
Mm9::chrX:133372612..133372625,+p@chrX:133372612..133372625
+
Mm9::chrX:133372643..133372665,+p@chrX:133372643..133372665
+


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:0022010myelination in the central nervous system0.00345148742672438
GO:0032291ensheathment of axons in the central nervous system0.00345148742672438
GO:0004308exo-alpha-sialidase activity0.00460185716771568
GO:0016997alpha-sialidase activity0.00493015603281988
GO:0042759long-chain fatty acid biosynthetic process0.00493015603281988
GO:0043209myelin sheath0.00493015603281988
GO:0014003oligodendrocyte development0.00493015603281988
GO:0021782glial cell development0.00766808104063517
GO:0048709oligodendrocyte differentiation0.00766808104063517
GO:0001676long-chain fatty acid metabolic process0.00966072314069902
GO:0042552myelination0.0153871323097943
GO:0008366axon ensheathment0.0153871323097943
GO:0007272ensheathment of neurons0.0153871323097943
GO:0001508regulation of action potential0.0174698111462984
GO:0010001glial cell differentiation0.0174698111462984
GO:0042063gliogenesis0.0176694901197512
GO:0006633fatty acid biosynthetic process0.0254899305412603
GO:0046394carboxylic acid biosynthetic process0.0254899305412603
GO:0016053organic acid biosynthetic process0.0254899305412603
GO:0048469cell maturation0.0254899305412603
GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds0.0284828166957132
GO:0021700developmental maturation0.0284828166957132
GO:0016798hydrolase activity, acting on glycosyl bonds0.0323189575174909
GO:0006631fatty acid metabolic process0.0458193843685796



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
neuron3.74e-1333
neuronal stem cell3.74e-1333
neuroblast3.74e-1333
electrically signaling cell3.74e-1333
ectodermal cell2.43e-1244
neurectodermal cell2.43e-1244
neural cell1.74e-1143
electrically responsive cell1.97e-1039
electrically active cell1.97e-1039
autonomic neuron4.02e-109
non-terminally differentiated cell1.80e-0949
raphe nuclei neuron2.89e-073

Uber Anatomy
Ontology termp-valuen
nervous system3.08e-3575
central nervous system1.08e-3273
ectoderm-derived structure3.30e-3095
ectoderm3.30e-3095
presumptive ectoderm3.30e-3095
regional part of nervous system1.42e-2554
neurectoderm8.13e-2364
neural plate8.13e-2364
presumptive neural plate8.13e-2364
neural tube1.58e-2252
neural rod1.58e-2252
future spinal cord1.58e-2252
neural keel1.58e-2252
ecto-epithelium2.86e-2073
occipital lobe3.46e-1810
visual cortex3.46e-1810
neocortex3.46e-1810
brain4.40e-1847
future brain4.40e-1847
gray matter1.35e-1734
regional part of brain5.96e-1746
structure with developmental contribution from neural crest2.73e-1492
brain grey matter1.76e-1329
regional part of telencephalon1.76e-1329
telencephalon1.76e-1329
anterior neural tube5.20e-1340
peripheral nervous system1.22e-1211
pre-chordal neural plate4.18e-1249
regional part of forebrain6.72e-1239
forebrain6.72e-1239
future forebrain6.72e-1239
regional part of cerebral cortex9.41e-1217
posterior neural tube2.63e-1112
chordal neural plate2.63e-1112
cerebral cortex9.80e-1121
cerebral hemisphere9.80e-1121
pallium9.80e-1121
autonomic nervous system4.02e-109
regional part of midbrain2.82e-084
midbrain2.82e-084
presumptive midbrain2.82e-084
midbrain neural tube2.82e-084
organ system subdivision6.69e-08194
spinal cord2.05e-076
dorsal region element2.05e-076
dorsum2.05e-076
raphe nuclei2.89e-073
reticular formation2.89e-073


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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