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MCL coexpression mm9:361: Difference between revisions

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{{MCL_coexpression_mm9
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activity;0.030392264285323;19270,245474!GO:0045175;basal protein localization;0.030392264285323;50884!GO:0030950;establishment and/or maintenance of actin cytoskeleton polarity;0.030392264285323;50884!GO:0003922;GMP synthase (glutamine-hydrolyzing) activity;0.030392264285323;229363!GO:0003921;GMP synthase activity;0.030392264285323;229363!GO:0032879;regulation of localization;0.030392264285323;50884!GO:0030952;establishment and/or maintenance of cytoskeleton polarity;0.030392264285323;50884!GO:0032880;regulation of protein localization;0.030392264285323;50884!GO:0016835;carbon-oxygen lyase activity;0.0321103085972842;19270,245474!GO:0007509;mesoderm migration;0.037392542559238;50884!GO:0008078;mesodermal cell migration;0.037392542559238;50884!GO:0007354;zygotic determination of anterior/posterior axis, embryo;0.037392542559238;50884!GO:0006421;asparaginyl-tRNA aminoacylation;0.037392542559238;70223!GO:0016874;ligase activity;0.0391467307563428;229363,70223,12234!GO:0005173;stem cell factor receptor binding;0.0418606881635714;114715!GO:0006177;GMP biosynthetic process;0.0418606881635714;229363!GO:0006399;tRNA metabolic process;0.0418606881635714;245474,70223!GO:0048570;notochord morphogenesis;0.0418606881635714;50884!GO:0046037;GMP metabolic process;0.0418606881635714;229363!GO:0048617;embryonic foregut morphogenesis;0.0418606881635714;50884!GO:0010172;embryonic body morphogenesis;0.0418606881635714;50884!GO:0000154;rRNA modification;0.0418606881635714;245474!GO:0030519;snoRNP binding;0.0418606881635714;245474!GO:0007440;foregut morphogenesis;0.0418606881635714;50884!GO:0000578;embryonic axis specification;0.0418606881635714;50884!GO:0031119;tRNA pseudouridine synthesis;0.0418606881635714;245474!GO:0008595;determination of anterior/posterior axis, embryo;0.0418606881635714;50884!GO:0010171;body morphogenesis;0.0418606881635714;50884!GO:0007351;tripartite regional subdivision;0.0418606881635714;50884!GO:0007350;blastoderm segmentation;0.0440654891570662;50884!GO:0048611;embryonic ectodermal gut development;0.0440654891570662;50884!GO:0048613;embryonic ectodermal gut morphogenesis;0.0440654891570662;50884!GO:0006400;tRNA modification;0.0440654891570662;245474!GO:0030903;notochord development;0.0440654891570662;50884!GO:0045176;apical protein localization;0.0440654891570662;50884!GO:0016829;lyase activity;0.0440654891570662;19270,245474!GO:0042074;cell migration involved in gastrulation;0.0440654891570662;50884!GO:0050821;protein stabilization;0.0440654891570662;50884!GO:0048558;embryonic gut morphogenesis;0.0440654891570662;50884!GO:0016884;carbon-nitrogen ligase activity, with glutamine as amido-N-donor;0.0440654891570662;229363!GO:0004730;pseudouridylate synthase activity;0.0440654891570662;245474!GO:0016879;ligase activity, forming carbon-nitrogen bonds;0.0440654891570662;229363,12234!GO:0043170;macromolecule metabolic process;0.0440654891570662;19270,245596,54678,50884,76594,245474,56397,70223,12234!GO:0048340;paraxial mesoderm morphogenesis;0.0440654891570662;50884!GO:0000188;inactivation of MAPK activity;0.0440654891570662;114715!GO:0031647;regulation of protein stability;0.0440654891570662;50884!GO:0001522;pseudouridine synthesis;0.0440654891570662;245474!GO:0048557;embryonic digestive tract morphogenesis;0.0440654891570662;50884!GO:0008105;asymmetric protein localization;0.0440654891570662;50884!GO:0044238;primary metabolic process;0.0440654891570662;50884,76594,245474,56397,70223,12234,19270,229363,245596,54678!GO:0044237;cellular metabolic process;0.0440654891570662;50884,76594,245474,56397,70223,12234,19270,229363,245596,54678!GO:0007439;ectodermal gut development;0.0440654891570662;50884!GO:0009168;purine ribonucleoside monophosphate biosynthetic process;0.0440654891570662;229363!GO:0009127;purine nucleoside monophosphate biosynthetic process;0.0440654891570662;229363!GO:0048567;ectodermal 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|gostat_on_MCL_coexpression=GO:0016836;hydro-lyase activity;0.030392264285323;19270,245474!GO:0045175;basal protein localization;0.030392264285323;50884!GO:0030950;establishment and/or maintenance of actin cytoskeleton polarity;0.030392264285323;50884!GO:0003922;GMP synthase (glutamine-hydrolyzing) activity;0.030392264285323;229363!GO:0003921;GMP synthase activity;0.030392264285323;229363!GO:0032879;regulation of localization;0.030392264285323;50884!GO:0030952;establishment and/or maintenance of cytoskeleton polarity;0.030392264285323;50884!GO:0032880;regulation of protein localization;0.030392264285323;50884!GO:0016835;carbon-oxygen lyase activity;0.0321103085972842;19270,245474!GO:0007509;mesoderm migration;0.037392542559238;50884!GO:0008078;mesodermal cell migration;0.037392542559238;50884!GO:0007354;zygotic determination of anterior/posterior axis, embryo;0.037392542559238;50884!GO:0006421;asparaginyl-tRNA aminoacylation;0.037392542559238;70223!GO:0016874;ligase activity;0.0391467307563428;229363,70223,12234!GO:0005173;stem cell factor receptor binding;0.0418606881635714;114715!GO:0006177;GMP biosynthetic process;0.0418606881635714;229363!GO:0006399;tRNA metabolic process;0.0418606881635714;245474,70223!GO:0048570;notochord morphogenesis;0.0418606881635714;50884!GO:0046037;GMP metabolic process;0.0418606881635714;229363!GO:0048617;embryonic foregut morphogenesis;0.0418606881635714;50884!GO:0010172;embryonic body morphogenesis;0.0418606881635714;50884!GO:0000154;rRNA modification;0.0418606881635714;245474!GO:0030519;snoRNP binding;0.0418606881635714;245474!GO:0007440;foregut morphogenesis;0.0418606881635714;50884!GO:0000578;embryonic axis specification;0.0418606881635714;50884!GO:0031119;tRNA pseudouridine synthesis;0.0418606881635714;245474!GO:0008595;determination of anterior/posterior axis, embryo;0.0418606881635714;50884!GO:0010171;body morphogenesis;0.0418606881635714;50884!GO:0007351;tripartite regional subdivision;0.0418606881635714;50884!GO:0007350;blastoderm segmentation;0.0440654891570662;50884!GO:0048611;embryonic ectodermal gut development;0.0440654891570662;50884!GO:0048613;embryonic ectodermal gut morphogenesis;0.0440654891570662;50884!GO:0006400;tRNA modification;0.0440654891570662;245474!GO:0030903;notochord development;0.0440654891570662;50884!GO:0045176;apical protein localization;0.0440654891570662;50884!GO:0016829;lyase activity;0.0440654891570662;19270,245474!GO:0042074;cell migration involved in gastrulation;0.0440654891570662;50884!GO:0050821;protein stabilization;0.0440654891570662;50884!GO:0048558;embryonic gut morphogenesis;0.0440654891570662;50884!GO:0016884;carbon-nitrogen ligase activity, with glutamine as amido-N-donor;0.0440654891570662;229363!GO:0004730;pseudouridylate synthase activity;0.0440654891570662;245474!GO:0016879;ligase activity, forming carbon-nitrogen bonds;0.0440654891570662;229363,12234!GO:0043170;macromolecule metabolic process;0.0440654891570662;19270,245596,54678,50884,76594,245474,56397,70223,12234!GO:0048340;paraxial mesoderm morphogenesis;0.0440654891570662;50884!GO:0000188;inactivation of MAPK activity;0.0440654891570662;114715!GO:0031647;regulation of protein stability;0.0440654891570662;50884!GO:0001522;pseudouridine synthesis;0.0440654891570662;245474!GO:0048557;embryonic digestive tract morphogenesis;0.0440654891570662;50884!GO:0008105;asymmetric protein localization;0.0440654891570662;50884!GO:0044238;primary metabolic process;0.0440654891570662;50884,76594,245474,56397,70223,12234,19270,229363,245596,54678!GO:0044237;cellular metabolic process;0.0440654891570662;50884,76594,245474,56397,70223,12234,19270,229363,245596,54678!GO:0007439;ectodermal gut development;0.0440654891570662;50884!GO:0009168;purine ribonucleoside monophosphate biosynthetic process;0.0440654891570662;229363!GO:0009127;purine nucleoside monophosphate biosynthetic process;0.0440654891570662;229363!GO:0048567;ectodermal gut morphogenesis;0.0440654891570662;50884!GO:0048547;gut morphogenesis;0.0451697183144582;50884!GO:0009167;purine ribonucleoside monophosphate metabolic process;0.0451697183144582;229363!GO:0009126;purine nucleoside monophosphate metabolic process;0.0451697183144582;229363!GO:0009948;anterior/posterior axis specification;0.0451697183144582;50884!GO:0048546;digestive tract morphogenesis;0.0491768801296322;50884!GO:0048339;paraxial mesoderm development;0.0491768801296322;50884!GO:0035050;embryonic heart tube development;0.0491768801296322;50884!GO:0048566;embryonic gut development;0.0491768801296322;50884!GO:0009156;ribonucleoside monophosphate biosynthetic process;0.0491768801296322;229363!
}}

Latest revision as of 15:10, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:12385975..12385998,+p4@Ptprg
Mm9::chr14:12386013..12386028,+p6@Ptprg
Mm9::chr18:35862724..35862735,-p3@Dnajc18
Mm9::chr18:35862738..35862753,-p1@Dnajc18
Mm9::chr18:38761259..38761273,+p2@Arhgap26
Mm9::chr18:64676201..64676219,-p2@Nars
Mm9::chr19:45438234..45438321,+p1@Btrc
Mm9::chr2:116946596..116946618,+p2@Spred1
Mm9::chr2:116946787..116946885,+p1@Spred1
Mm9::chr2:121692654..121692733,+p1@Casc4
Mm9::chr2:80421372..80421385,-p5@Nckap1
Mm9::chr2:80421391..80421423,-p2@Nckap1
Mm9::chr2:80421429..80421450,-p3@Nckap1
Mm9::chr3:63780031..63780057,+p2@Gmps
Mm9::chr7:25039763..25039831,+p1@Zfp108
Mm9::chr7:99890142..99890225,+p1@Rab30
Mm9::chrX:108810678..108810736,-p1@Hdx
Mm9::chrX:131252469..131252480,+p2@Armcx1
Mm9::chrX:131252482..131252557,+p1@Armcx1
Mm9::chrX:133275818..133275846,-p1@Morf4l2
Mm9::chrX:72341224..72341261,+p2@Dkc1
Mm9::chrX:92906980..92907024,+p2@Zc3h12b


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:0016836hydro-lyase activity0.030392264285323
GO:0045175basal protein localization0.030392264285323
GO:0030950establishment and/or maintenance of actin cytoskeleton polarity0.030392264285323
GO:0003922GMP synthase (glutamine-hydrolyzing) activity0.030392264285323
GO:0003921GMP synthase activity0.030392264285323
GO:0032879regulation of localization0.030392264285323
GO:0030952establishment and/or maintenance of cytoskeleton polarity0.030392264285323
GO:0032880regulation of protein localization0.030392264285323
GO:0016835carbon-oxygen lyase activity0.0321103085972842
GO:0007509mesoderm migration0.037392542559238
GO:0008078mesodermal cell migration0.037392542559238
GO:0007354zygotic determination of anterior/posterior axis, embryo0.037392542559238
GO:0006421asparaginyl-tRNA aminoacylation0.037392542559238
GO:0016874ligase activity0.0391467307563428
GO:0005173stem cell factor receptor binding0.0418606881635714
GO:0006177GMP biosynthetic process0.0418606881635714
GO:0006399tRNA metabolic process0.0418606881635714
GO:0048570notochord morphogenesis0.0418606881635714
GO:0046037GMP metabolic process0.0418606881635714
GO:0048617embryonic foregut morphogenesis0.0418606881635714
GO:0010172embryonic body morphogenesis0.0418606881635714
GO:0000154rRNA modification0.0418606881635714
GO:0030519snoRNP binding0.0418606881635714
GO:0007440foregut morphogenesis0.0418606881635714
GO:0000578embryonic axis specification0.0418606881635714
GO:0031119tRNA pseudouridine synthesis0.0418606881635714
GO:0008595determination of anterior/posterior axis, embryo0.0418606881635714
GO:0010171body morphogenesis0.0418606881635714
GO:0007351tripartite regional subdivision0.0418606881635714
GO:0007350blastoderm segmentation0.0440654891570662
GO:0048611embryonic ectodermal gut development0.0440654891570662
GO:0048613embryonic ectodermal gut morphogenesis0.0440654891570662
GO:0006400tRNA modification0.0440654891570662
GO:0030903notochord development0.0440654891570662
GO:0045176apical protein localization0.0440654891570662
GO:0016829lyase activity0.0440654891570662
GO:0042074cell migration involved in gastrulation0.0440654891570662
GO:0050821protein stabilization0.0440654891570662
GO:0048558embryonic gut morphogenesis0.0440654891570662
GO:0016884carbon-nitrogen ligase activity, with glutamine as amido-N-donor0.0440654891570662
GO:0004730pseudouridylate synthase activity0.0440654891570662
GO:0016879ligase activity, forming carbon-nitrogen bonds0.0440654891570662
GO:0043170macromolecule metabolic process0.0440654891570662
GO:0048340paraxial mesoderm morphogenesis0.0440654891570662
GO:0000188inactivation of MAPK activity0.0440654891570662
GO:0031647regulation of protein stability0.0440654891570662
GO:0001522pseudouridine synthesis0.0440654891570662
GO:0048557embryonic digestive tract morphogenesis0.0440654891570662
GO:0008105asymmetric protein localization0.0440654891570662
GO:0044238primary metabolic process0.0440654891570662
GO:0044237cellular metabolic process0.0440654891570662
GO:0007439ectodermal gut development0.0440654891570662
GO:0009168purine ribonucleoside monophosphate biosynthetic process0.0440654891570662
GO:0009127purine nucleoside monophosphate biosynthetic process0.0440654891570662
GO:0048567ectodermal gut morphogenesis0.0440654891570662
GO:0048547gut morphogenesis0.0451697183144582
GO:0009167purine ribonucleoside monophosphate metabolic process0.0451697183144582
GO:0009126purine nucleoside monophosphate metabolic process0.0451697183144582
GO:0009948anterior/posterior axis specification0.0451697183144582
GO:0048546digestive tract morphogenesis0.0491768801296322
GO:0048339paraxial mesoderm development0.0491768801296322
GO:0035050embryonic heart tube development0.0491768801296322
GO:0048566embryonic gut development0.0491768801296322
GO:0009156ribonucleoside monophosphate biosynthetic process0.0491768801296322



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
structure with developmental contribution from neural crest8.17e-2092
neurectoderm1.61e-1964
neural plate1.61e-1964
presumptive neural plate1.61e-1964
ecto-epithelium7.26e-1873
ectoderm-derived structure6.06e-1795
ectoderm6.06e-1795
presumptive ectoderm6.06e-1795
regional part of nervous system1.05e-1654
central nervous system1.91e-1673
nervous system4.55e-1675
pre-chordal neural plate1.22e-1549
neural tube1.36e-1552
neural rod1.36e-1552
future spinal cord1.36e-1552
neural keel1.36e-1552
brain7.10e-1447
future brain7.10e-1447
regional part of brain2.59e-1346
anterior neural tube2.60e-1240
regional part of forebrain1.13e-1139
forebrain1.13e-1139
future forebrain1.13e-1139
multi-cellular organism8.88e-11333
gray matter2.99e-1034
tube3.28e-10114
anatomical conduit7.62e-10122
brain grey matter9.65e-0929
regional part of telencephalon9.65e-0929
telencephalon9.65e-0929
embryo2.60e-08320
occipital lobe1.96e-0710
visual cortex1.96e-0710
neocortex1.96e-0710


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)
MA0003.13.88361
MA0004.10.444991
MA0006.10.789557
MA0007.10.421767
MA0009.12.10566
MA0014.11.9467
MA0017.10.0678809
MA0019.10.329708
MA0024.10.445298
MA0025.10.694475
MA0027.12.07936
MA0028.10.825855
MA0029.10.426655
MA0030.10.43227
MA0031.10.402033
MA0038.10.243815
MA0040.10.494317
MA0041.10.10094
MA0042.10.0939798
MA0043.10.569356
MA0046.10.514989
MA0048.11.15341
MA0050.10.169675
MA0051.10.250459
MA0052.10.501416
MA0055.10.83588
MA0056.10
MA0057.10.327386
MA0058.10.303016
MA0059.10.0968666
MA0060.11.20594
MA0061.10.618873
MA0063.10
MA0066.10.235725
MA0067.10.798606
MA0068.11.42842
MA0069.10.501715
MA0070.10.493176
MA0071.10.974672
MA0072.10.485733
MA0073.10.220189
MA0074.10.209912
MA0076.10.0767377
MA0077.10.466808
MA0078.10.275441
MA0081.10.717402
MA0083.10.568641
MA0084.11.11388
MA0087.10.530004
MA0088.11.98379
MA0089.10
MA0090.10.124244
MA0091.10.153118
MA0092.10.124428
MA0093.10.496926
MA0095.10
MA0098.10
MA0100.11.10548
MA0101.10.101635
MA0103.10.0728209
MA0105.11.47579
MA0106.10.281418
MA0107.10.526347
MA0108.20.348212
MA0109.10
MA0111.10.132626
MA0113.10.259904
MA0114.10.145706
MA0115.10.571881
MA0116.10.0563303
MA0117.10.542889
MA0119.10.333984
MA0122.10.560692
MA0124.10.748494
MA0125.10.67944
MA0130.10
MA0131.11.56694
MA0132.10
MA0133.10
MA0135.10.602346
MA0136.10.637057
MA0139.11.40989
MA0140.10.201717
MA0141.10.0822433
MA0142.10.389844
MA0143.10.27232
MA0144.10.344625
MA0145.10.564602
MA0146.10.387238
MA0147.10.0420513
MA0148.10.470482
MA0149.10.104621
MA0062.21.1429
MA0035.20.205003
MA0039.21.11708
MA0138.20.319705
MA0002.20.0910543
MA0137.20.581412
MA0104.20.103917
MA0047.20.243248
MA0112.20.371859
MA0065.20.0491972
MA0150.10.833976
MA0151.10
MA0152.10.243327
MA0153.10.617506
MA0154.10.571068
MA0155.10.438423
MA0156.10.263883
MA0157.10.363212
MA0158.10
MA0159.10.392761
MA0160.10.475244
MA0161.10
MA0162.13.75527
MA0163.12.0793
MA0164.10.224368
MA0080.20.528447
MA0018.20.654151
MA0099.20.844851
MA0079.21.21639
MA0102.21.16504
MA0258.10.131525
MA0259.10.626539
MA0442.10
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