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MCL coexpression mm9:866: Difference between revisions

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{{MCL_coexpression_mm9
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B activity;0.0426800538728488;13030!GO:0005764;lysosome;0.0426800538728488;13030,19156!GO:0000323;lytic vacuole;0.0426800538728488;13030,19156!GO:0005773;vacuole;0.0426800538728488;13030,19156!GO:0008047;enzyme activator activity;0.0426800538728488;76795,21858!GO:0030814;regulation of cAMP metabolic process;0.0426800538728488;21858!GO:0008191;metalloendopeptidase inhibitor activity;0.0426800538728488;21858!GO:0030799;regulation of cyclic nucleotide metabolic process;0.0426800538728488;21858!GO:0050790;regulation of catalytic activity;0.0426800538728488;13030,76795!GO:0005385;zinc ion transmembrane transporter activity;0.0426800538728488;106947!GO:0006140;regulation of nucleotide metabolic process;0.0426800538728488;21858!GO:0065009;regulation of a molecular function;0.0478674488936791;13030,76795!GO:0015299;solute:hydrogen antiporter activity;0.0478674488936791;234076!GO:0009966;regulation of signal transduction;0.0478674488936791;76795,21858!GO:0043408;regulation of MAPKKK cascade;0.0485669984857689;21858!GO:0006885;regulation of pH;0.0485669984857689;234076!GO:0015298;solute:cation antiporter activity;0.0485669984857689;234076!GO:0046058;cAMP metabolic process;0.0485669984857689;21858!GO:0015300;solute:solute antiporter activity;0.0485669984857689;234076!GO:0005178;integrin binding;0.0485669984857689;21858!GO:0006829;zinc ion transport;0.0485669984857689;106947!GO:0046915;transition metal ion transmembrane transporter activity;0.0485669984857689;106947!GO:0008324;cation transmembrane transporter activity;0.0485669984857689;234076,106947!GO:0045664;regulation of neuron differentiation;0.0485669984857689;21858!GO:0032313;regulation of Rab GTPase activity;0.0485669984857689;76795!GO:0032483;regulation of Rab protein signal transduction;0.0485669984857689;76795!GO:0032482;Rab protein signal 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|gostat_on_MCL_coexpression=GO:0004213;cathepsin B activity;0.0426800538728488;13030!GO:0005764;lysosome;0.0426800538728488;13030,19156!GO:0000323;lytic vacuole;0.0426800538728488;13030,19156!GO:0005773;vacuole;0.0426800538728488;13030,19156!GO:0008047;enzyme activator activity;0.0426800538728488;76795,21858!GO:0030814;regulation of cAMP metabolic process;0.0426800538728488;21858!GO:0008191;metalloendopeptidase inhibitor activity;0.0426800538728488;21858!GO:0030799;regulation of cyclic nucleotide metabolic process;0.0426800538728488;21858!GO:0050790;regulation of catalytic activity;0.0426800538728488;13030,76795!GO:0005385;zinc ion transmembrane transporter activity;0.0426800538728488;106947!GO:0006140;regulation of nucleotide metabolic process;0.0426800538728488;21858!GO:0065009;regulation of a molecular function;0.0478674488936791;13030,76795!GO:0015299;solute:hydrogen antiporter activity;0.0478674488936791;234076!GO:0009966;regulation of signal transduction;0.0478674488936791;76795,21858!GO:0043408;regulation of MAPKKK cascade;0.0485669984857689;21858!GO:0006885;regulation of pH;0.0485669984857689;234076!GO:0015298;solute:cation antiporter activity;0.0485669984857689;234076!GO:0046058;cAMP metabolic process;0.0485669984857689;21858!GO:0015300;solute:solute antiporter activity;0.0485669984857689;234076!GO:0005178;integrin binding;0.0485669984857689;21858!GO:0006829;zinc ion transport;0.0485669984857689;106947!GO:0046915;transition metal ion transmembrane transporter activity;0.0485669984857689;106947!GO:0008324;cation transmembrane transporter activity;0.0485669984857689;234076,106947!GO:0045664;regulation of neuron differentiation;0.0485669984857689;21858!GO:0032313;regulation of Rab GTPase activity;0.0485669984857689;76795!GO:0032483;regulation of Rab protein signal transduction;0.0485669984857689;76795!GO:0032482;Rab protein signal transduction;0.0485669984857689;76795!
|ontology_enrichment_celltype=CL:0000055!9.97e-13!49;CL:0000221!2.24e-10!44;CL:0000133!2.24e-10!44;CL:0002319!3.95e-10!43;CL:0000393!4.11e-08!39;CL:0000211!4.11e-08!39;CL:0002321!1.30e-07!70
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!3.21e-22!75;UBERON:0001017!1.62e-21!73;UBERON:0004121!1.17e-17!95;UBERON:0000924!1.17e-17!95;UBERON:0006601!1.17e-17!95;UBERON:0000073!2.17e-17!54;UBERON:0001049!2.45e-16!52;UBERON:0005068!2.45e-16!52;UBERON:0006241!2.45e-16!52;UBERON:0007135!2.45e-16!52;UBERON:0000955!3.01e-14!47;UBERON:0006238!3.01e-14!47;UBERON:0002616!7.85e-14!46;UBERON:0010314!5.61e-13!92;UBERON:0002346!2.75e-12!64;UBERON:0003075!2.75e-12!64;UBERON:0007284!2.75e-12!64;UBERON:0002020!1.59e-11!34;UBERON:0010371!3.23e-11!73;UBERON:0003080!6.23e-11!40;UBERON:0002780!2.18e-10!39;UBERON:0001890!2.18e-10!39;UBERON:0006240!2.18e-10!39;UBERON:0003528!8.73e-10!29;UBERON:0002791!8.73e-10!29;UBERON:0001893!8.73e-10!29;UBERON:0004111!3.75e-09!122;UBERON:0000025!3.68e-08!114;UBERON:0003056!9.32e-08!49;UBERON:0002619!1.20e-07!17;UBERON:0000956!2.51e-07!21;UBERON:0001869!2.51e-07!21;UBERON:0000203!2.51e-07!21;UBERON:0002021!5.02e-07!10;UBERON:0000411!5.02e-07!10;UBERON:0001950!5.02e-07!10;UBERON:0007023!5.76e-07!51
}}

Latest revision as of 16:01, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:59740429..59740440,+p2@Psap
Mm9::chr10:80500045..80500084,-p1@Slc39a3
Mm9::chr11:118216683..118216691,-p2@Timp2
Mm9::chr11:49944844..49944928,+p1@Tbc1d9b
Mm9::chr14:63741287..63741296,+p4@Ctsb
Mm9::chr14:63741303..63741314,+p3@Ctsb
Mm9::chr2:155644932..155645005,-p1@BC029722
Mm9::chr8:13288173..13288220,+p1@Tmco3


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:0004213cathepsin B activity0.0426800538728488
GO:0005764lysosome0.0426800538728488
GO:0000323lytic vacuole0.0426800538728488
GO:0005773vacuole0.0426800538728488
GO:0008047enzyme activator activity0.0426800538728488
GO:0030814regulation of cAMP metabolic process0.0426800538728488
GO:0008191metalloendopeptidase inhibitor activity0.0426800538728488
GO:0030799regulation of cyclic nucleotide metabolic process0.0426800538728488
GO:0050790regulation of catalytic activity0.0426800538728488
GO:0005385zinc ion transmembrane transporter activity0.0426800538728488
GO:0006140regulation of nucleotide metabolic process0.0426800538728488
GO:0065009regulation of a molecular function0.0478674488936791
GO:0015299solute:hydrogen antiporter activity0.0478674488936791
GO:0009966regulation of signal transduction0.0478674488936791
GO:0043408regulation of MAPKKK cascade0.0485669984857689
GO:0006885regulation of pH0.0485669984857689
GO:0015298solute:cation antiporter activity0.0485669984857689
GO:0046058cAMP metabolic process0.0485669984857689
GO:0015300solute:solute antiporter activity0.0485669984857689
GO:0005178integrin binding0.0485669984857689
GO:0006829zinc ion transport0.0485669984857689
GO:0046915transition metal ion transmembrane transporter activity0.0485669984857689
GO:0008324cation transmembrane transporter activity0.0485669984857689
GO:0045664regulation of neuron differentiation0.0485669984857689
GO:0032313regulation of Rab GTPase activity0.0485669984857689
GO:0032483regulation of Rab protein signal transduction0.0485669984857689
GO:0032482Rab protein signal transduction0.0485669984857689



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
non-terminally differentiated cell9.97e-1349
ectodermal cell2.24e-1044
neurectodermal cell2.24e-1044
neural cell3.95e-1043
electrically responsive cell4.11e-0839
electrically active cell4.11e-0839
embryonic cell1.30e-0770

Uber Anatomy
Ontology termp-valuen
nervous system3.21e-2275
central nervous system1.62e-2173
ectoderm-derived structure1.17e-1795
ectoderm1.17e-1795
presumptive ectoderm1.17e-1795
regional part of nervous system2.17e-1754
neural tube2.45e-1652
neural rod2.45e-1652
future spinal cord2.45e-1652
neural keel2.45e-1652
brain3.01e-1447
future brain3.01e-1447
regional part of brain7.85e-1446
structure with developmental contribution from neural crest5.61e-1392
neurectoderm2.75e-1264
neural plate2.75e-1264
presumptive neural plate2.75e-1264
gray matter1.59e-1134
ecto-epithelium3.23e-1173
anterior neural tube6.23e-1140
regional part of forebrain2.18e-1039
forebrain2.18e-1039
future forebrain2.18e-1039
brain grey matter8.73e-1029
regional part of telencephalon8.73e-1029
telencephalon8.73e-1029
anatomical conduit3.75e-09122
tube3.68e-08114
pre-chordal neural plate9.32e-0849
regional part of cerebral cortex1.20e-0717
cerebral cortex2.51e-0721
cerebral hemisphere2.51e-0721
pallium2.51e-0721
occipital lobe5.02e-0710
visual cortex5.02e-0710
neocortex5.02e-0710
adult organism5.76e-0751


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)
MA0003.11.81836
MA0004.11.10905
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.11.16295
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.769859
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.11.66702
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.282934
MA0056.10
MA0057.10.31126
MA0058.10.90507
MA0059.10.353484
MA0060.10.197678
MA0061.11.19505
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.319589
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.0449725
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.11.29043
MA0089.10
MA0090.11.03628
MA0091.10.447561
MA0092.10.401504
MA0093.11.43515
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.950493
MA0103.10.307078
MA0105.10.41549
MA0106.10.626997
MA0107.10.814533
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.14.53803
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.12.22005
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.11.35361
MA0146.12.18849
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.84271
MA0035.20.524137
MA0039.22.43328
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.20.0701537
MA0065.20.0704227
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.677425
MA0155.10.0804339
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.439322
MA0163.10.212034
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.431684
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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