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MCL coexpression mm9:361: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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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!
}}
}}

Revision as of 12:40, 11 October 2012


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>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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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