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MCL coexpression mm9:602: Difference between revisions

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{{MCL_coexpression_mm9
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filament bundle assembly;0.0135519871096006;380684!GO:0005883;neurofilament;0.0135519871096006;380684!GO:0060052;neurofilament cytoskeleton organization and biogenesis;0.0135519871096006;380684!GO:0060053;neurofilament cytoskeleton;0.0135519871096006;380684!GO:0045109;intermediate filament organization;0.0135519871096006;380684!GO:0032011;ARF protein signal transduction;0.0135519871096006;232227!GO:0005086;ARF guanyl-nucleotide exchange factor activity;0.0135519871096006;232227!GO:0032012;regulation of ARF protein signal transduction;0.0135519871096006;232227!GO:0045104;intermediate filament cytoskeleton organization and biogenesis;0.0186107506779222;380684!GO:0045103;intermediate filament-based 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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0.082475037168298,0,0.034318863244337,0.0166660626832929,0,0,0,0,0,0,0,0,0.11292479074727,0.0205563265474198,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0400093965272457,0,0,0,0,0,0,0,0,0,0,0,0,0.480466514906996,0.41662635992513,0,0,0,0.706500136822058,0.647699018292791,0.857809724751752,0,0.0190094117790312,0,0.803587571002431,0.260679637160558,0.62969106586328,0.423968249646902,0.484124355765587,0.137606919870727,0,0,0,0,0,0,0,0,0.0048531789482942,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0192453400108068,0,0,0,0,0,0,0,0,0.268433791687647,0.238020128913375,0,0,0,0,0.456524204885504,0.222888897389984,0.0257025274002712,0.0696031033168343,0.0499886982764315,0.459760956901303,0.366448207886406,0,0,0,0,0,0,0,0.0609639314262262,0.0285860945550467,0,0.0388988969149198,0.140512702207538,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0828894264954325,0.00951980514229275,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.648468704314205,0.676632147595059,0,0,0,0,0,0,0,0,0,0,0,0.060504220684743,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0763100310951818,0.0459548542215198,0.115432414129512,0,0,0,0,0,0,0,0,0,0.786614726518432,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.016597321936113,0.0265784939468031,0.0412369799760303,0,0,0,0,0,0,0,0,0,0,0.0208870423994129,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.199118276428015,0.216853801753665,0.092444625090153,0.112688731369336,0.0955204645867891,0,0.06310778060851,0.0992102666174571,0.172345441322589,0.181203192176975,0,0,0,0,0,0,0,0,0,0,0,0,0.0388749848471105,0,0.0242538736058389,0,0,0,0,0,0,0.0354759961767123,0,0,0,0,0,0,0,0,0.0486884105045233,0.0408018333703219,0,0,0,0,0,0,0.0156801069410981,0,0
|gostat_on_MCL_coexpression=GO:0045110;intermediate filament bundle assembly;0.0135519871096006;380684!GO:0005883;neurofilament;0.0135519871096006;380684!GO:0060052;neurofilament cytoskeleton organization and biogenesis;0.0135519871096006;380684!GO:0060053;neurofilament cytoskeleton;0.0135519871096006;380684!GO:0045109;intermediate filament organization;0.0135519871096006;380684!GO:0032011;ARF protein signal transduction;0.0135519871096006;232227!GO:0005086;ARF guanyl-nucleotide exchange factor activity;0.0135519871096006;232227!GO:0032012;regulation of ARF protein signal transduction;0.0135519871096006;232227!GO:0045104;intermediate filament cytoskeleton organization and biogenesis;0.0186107506779222;380684!GO:0045103;intermediate filament-based process;0.0197022609843965;380684!
|ontology_enrichment_celltype=CL:0000117!5.28e-10!23;CL:0000337!5.28e-10!23
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!5.52e-32!54;UBERON:0001049!6.12e-29!52;UBERON:0005068!6.12e-29!52;UBERON:0006241!6.12e-29!52;UBERON:0007135!6.12e-29!52;UBERON:0002346!4.49e-28!64;UBERON:0003075!4.49e-28!64;UBERON:0007284!4.49e-28!64;UBERON:0001017!1.32e-25!73;UBERON:0001016!1.26e-24!75;UBERON:0010371!2.78e-23!73;UBERON:0004121!5.25e-22!95;UBERON:0000924!5.25e-22!95;UBERON:0006601!5.25e-22!95;UBERON:0000955!7.19e-22!47;UBERON:0006238!7.19e-22!47;UBERON:0002616!8.32e-21!46;UBERON:0002020!1.40e-19!34;UBERON:0003056!3.98e-18!49;UBERON:0010314!2.56e-17!92;UBERON:0003080!5.82e-17!40;UBERON:0002780!9.62e-16!39;UBERON:0001890!9.62e-16!39;UBERON:0006240!9.62e-16!39;UBERON:0003076!1.53e-13!12;UBERON:0003057!1.53e-13!12;UBERON:0003528!3.02e-13!29;UBERON:0002791!3.02e-13!29;UBERON:0001893!3.02e-13!29;UBERON:0002021!1.18e-11!10;UBERON:0000411!1.18e-11!10;UBERON:0001950!1.18e-11!10;UBERON:0002240!1.19e-10!6;UBERON:0005174!1.19e-10!6;UBERON:0001137!1.19e-10!6;UBERON:0001948!5.48e-09!5;UBERON:0002315!5.48e-09!5;UBERON:0002619!6.76e-09!17;UBERON:0000956!4.31e-08!21;UBERON:0001869!4.31e-08!21;UBERON:0000203!4.31e-08!21;UBERON:0000025!4.64e-08!114;UBERON:0002950!8.47e-08!4;UBERON:0001891!8.47e-08!4;UBERON:0009616!8.47e-08!4;UBERON:0010286!8.47e-08!4;UBERON:0004111!5.74e-07!122;UBERON:0002420!8.05e-07!8;UBERON:0007245!8.05e-07!8;UBERON:0010009!8.05e-07!8;UBERON:0010011!8.05e-07!8;UBERON:0000454!8.05e-07!8
}}

Latest revision as of 15:35, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:4839624..4839635,-p@chr11:4839624..4839635
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Mm9::chr11:4839683..4839697,-p@chr11:4839683..4839697
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Mm9::chr11:4839712..4839727,-p@chr11:4839712..4839727
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Mm9::chr11:4839812..4839821,-p@chr11:4839812..4839821
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Mm9::chr11:4839936..4839944,-p@chr11:4839936..4839944
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Mm9::chr11:4840044..4840053,-p@chr11:4840044..4840053
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Mm9::chr11:4841397..4841408,-p@chr11:4841397..4841408
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Mm9::chr11:4843926..4843937,-p@chr11:4843926..4843937
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Mm9::chr2:103659822..103659827,-p1@ENSMUST00000118421
p1@ENSMUST00000167989
Mm9::chr6:90686750..90686771,-p7@Iqsec1
Mm9::chr6:90686772..90686811,-p2@Iqsec1
Mm9::chrX:53984619..53984648,+p8@Fhl1


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:0045110intermediate filament bundle assembly0.0135519871096006
GO:0005883neurofilament0.0135519871096006
GO:0060052neurofilament cytoskeleton organization and biogenesis0.0135519871096006
GO:0060053neurofilament cytoskeleton0.0135519871096006
GO:0045109intermediate filament organization0.0135519871096006
GO:0032011ARF protein signal transduction0.0135519871096006
GO:0005086ARF guanyl-nucleotide exchange factor activity0.0135519871096006
GO:0032012regulation of ARF protein signal transduction0.0135519871096006
GO:0045104intermediate filament cytoskeleton organization and biogenesis0.0186107506779222
GO:0045103intermediate filament-based process0.0197022609843965



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
CNS neuron (sensu Vertebrata)5.28e-1023
neuroblast (sensu Vertebrata)5.28e-1023

Uber Anatomy
Ontology termp-valuen
regional part of nervous system5.52e-3254
neural tube6.12e-2952
neural rod6.12e-2952
future spinal cord6.12e-2952
neural keel6.12e-2952
neurectoderm4.49e-2864
neural plate4.49e-2864
presumptive neural plate4.49e-2864
central nervous system1.32e-2573
nervous system1.26e-2475
ecto-epithelium2.78e-2373
ectoderm-derived structure5.25e-2295
ectoderm5.25e-2295
presumptive ectoderm5.25e-2295
brain7.19e-2247
future brain7.19e-2247
regional part of brain8.32e-2146
gray matter1.40e-1934
pre-chordal neural plate3.98e-1849
structure with developmental contribution from neural crest2.56e-1792
anterior neural tube5.82e-1740
regional part of forebrain9.62e-1639
forebrain9.62e-1639
future forebrain9.62e-1639
posterior neural tube1.53e-1312
chordal neural plate1.53e-1312
brain grey matter3.02e-1329
regional part of telencephalon3.02e-1329
telencephalon3.02e-1329
occipital lobe1.18e-1110
visual cortex1.18e-1110
neocortex1.18e-1110
spinal cord1.19e-106
dorsal region element1.19e-106
dorsum1.19e-106
regional part of spinal cord5.48e-095
gray matter of spinal cord5.48e-095
regional part of cerebral cortex6.76e-0917
cerebral cortex4.31e-0821
cerebral hemisphere4.31e-0821
pallium4.31e-0821
tube4.64e-08114
regional part of midbrain8.47e-084
midbrain8.47e-084
presumptive midbrain8.47e-084
midbrain neural tube8.47e-084
anatomical conduit5.74e-07122
basal ganglion8.05e-078
nuclear complex of neuraxis8.05e-078
aggregate regional part of brain8.05e-078
collection of basal ganglia8.05e-078
cerebral subcortex8.05e-078


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)
MA0003.10.307389
MA0004.10.303605
MA0006.10.960584
MA0007.10.290695
MA0009.12.83734
MA0014.10.109847
MA0017.10.186015
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.10.173587
MA0029.11.55834
MA0030.10.65267
MA0031.10.618697
MA0038.10.432665
MA0040.10.721328
MA0041.10.239557
MA0042.10.228771
MA0043.10.802848
MA0046.10.743934
MA0048.10.680396
MA0050.10.337476
MA0051.10.440863
MA0052.10.729105
MA0055.10.00695701
MA0056.10
MA0057.10.151898
MA0058.10.223242
MA0059.11.22696
MA0060.10.108526
MA0061.12.55771
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.10.0405002
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.10.010504
MA0074.10.390075
MA0076.10.582294
MA0077.10.691048
MA0078.10.471303
MA0081.10.252371
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.10.24301
MA0089.10
MA0090.10.27428
MA0091.10.315003
MA0092.10.274547
MA0093.10.179936
MA0095.10
MA0098.10
MA0100.10.379666
MA0101.12.72599
MA0103.10.566591
MA0105.10.491577
MA0106.10.478503
MA0107.12.3671
MA0108.20.557195
MA0109.10
MA0111.10.286331
MA0113.10.452439
MA0114.10.127366
MA0115.10.805567
MA0116.10.165534
MA0117.10.774259
MA0119.10.241106
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.10.0883913
MA0140.10.379562
MA0141.11.13771
MA0142.10.604892
MA0143.10.467531
MA0144.10.406018
MA0145.10.109043
MA0146.11.21003
MA0147.10.138228
MA0148.10.317692
MA0149.10.245177
MA0062.20.235333
MA0035.20.383789
MA0039.20.0528941
MA0138.20.523978
MA0002.20.627335
MA0137.20.207733
MA0104.20.099275
MA0047.20.431964
MA0112.20.264932
MA0065.20.0259098
MA0150.10.790482
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.10.670722
MA0155.10.555224
MA0156.10.200311
MA0157.10.574484
MA0158.10
MA0159.10.145521
MA0160.10.85749
MA0161.10
MA0162.10.317256
MA0163.10.287849
MA0164.10.408402
MA0080.20.190316
MA0018.21.07118
MA0099.21.28797
MA0079.20.000845002
MA0102.21.42135
MA0258.10.376353
MA0259.10.130633
MA0442.10
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