{"data":{"id":"10.6084/m9.figshare.1281372","type":"dois","attributes":{"doi":"10.6084/m9.figshare.1281372","prefix":"10.6084","suffix":"m9.figshare.1281372","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Supek, Fran","nameType":"Personal","givenName":"Fran","familyName":"Supek","affiliation":[],"nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0000-0002-7811-6711","nameIdentifierScheme":"ORCID"}]}],"titles":[{"title":"Inferring gene function from evolutionary change in signatures of translation efficiency"}],"publisher":"figshare","container":{},"publicationYear":2015,"subjects":[{"subject":"Computational Biology"},{"subject":"60102 Bioinformatics","subjectScheme":"FOR"},{"subject":"FOS: Computer and information sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Computer and information sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Genetics"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Biological sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Microbiology"}],"contributors":[],"dates":[{"date":"2014-12-30","dateType":"Created"},{"date":"2015-01-01","dateType":"Updated"},{"date":"2015","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":["299041 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"\u003cstrong\u003eKrisko, Copic, Gabaldon, Lehner and Supek. Genome Biol 2014.\u003c/strong\u003e doi:10.1186/gb-2014-15-3-r44\u003cbr\u003e\u003cstrong\u003e\"Inferring gene function from evolutionary change in signatures of translation efficiency\"\u003c/strong\u003e Additional file 18. All COG gene families found to be significantly enriched/depleted for\u003cbr\u003ehighly expressed (HE) genes across 911 microbial genomes in any of the 24 examined\u003cbr\u003ephenotypes or environments. The HE genes were determined by quantifying the use of\u003cbr\u003eoptimal codons, which was compared against the composition of intergenic DNA\u003cbr\u003eusing a randomization test. \u003cstrong\u003e(Table A)\u003c/strong\u003e All 200 shown expression-phenotype links have (i) Fisher's exact test\u003cbr\u003efor enrichment P\u0026lt;0.01, (ii) magnitude of enrichment \u0026gt;2x or \u0026lt;0.5x, and\u003cbr\u003e(iii) Random Forest (RF) randomization test for confounding\u003cbr\u003ephenotypes/environments/phylogeny P\u0026lt;0.01. A total of 187 unique COGs are\u003cbr\u003erepresented in the list. The \"numOrgs\" column shows a number of organisms positive for the given trait,\u003cbr\u003eand the total number of organisms where that trait is defined. For instance,\u003cbr\u003etraits named \"Mammalian pathogen: (tissue or organ)\" are positive for pathogens\u003cbr\u003einfecting that organ, negative for all other mammalian pathogens,\u003cbr\u003eand undefined for the rest of examined Bacteria and Archaea. In some cases\u003cbr\u003e(e.g. halophiles), many microbes have undefined values due to missing annotations. In every COG, column \"a\" is the number of HE genes in microbes positive for the given trait,\u003cbr\u003e\"b\" is the count of non-HE genes in the same microbes, \"c\" is HE genes in microbes where\u003cbr\u003ethe trait is negative and \"d\" is the count of non-HE genes in the negative organisms.\u003cbr\u003e\"Enrich\" is the enrichment = a/(a+b) / ( c/(c+d) ). \u003cstrong\u003e(Table B)\u003c/strong\u003e Same as table A, but with the threshold for the RF test for counfounders\u003cbr\u003eslightly relaxed to P\u0026lt;0.05, yielding 167 additional COG-phenotype links (total: 367). \u003cstrong\u003e(Table C)\u003c/strong\u003e A set of 2386 inferred COG-phenotype links with broader coverage due to relaxed\u003cbr\u003ecriteria for magnitude of enrichment (1.5x or 0.66x, instead of 2x or 0.5x); the criteria\u003cbr\u003efor significance of the enrichment remained the same (P\u0026lt;0.01 in Fisher's exact test).\u003cbr\u003eAdditionally, the COG-phenotype links in this table did not have to pass the\u003cbr\u003eRF randomization test for confounders (meaning there is no control for phylogeny,\u003cbr\u003egenome size/GC content, or the inter-correlation of phenotypes).","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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