List of 551 paralogous Saccharomyces cerevisiae gene pairs formed by Whole Genome Duplication (WGD) or ohnolog pairs.
YEASTOHNOLOG is a dataframe of 551 paired genes. The first two
columns are the ohnolog gene pairs (systematic gene names). The third
column is an index (numeric) of the rate of sequence evolution. The
last two columns define the chromosome location.
Systematic gene names of the ohnolog pairs
Coefficient that represents the extent of non-synonymous sequence divergence between each ohnolog pairs (Yang and Nielsen, 2000). The highest is the coefficient the fastest the 2 elements of a pair have diverged.
Chromosome location of the each element of a pair. Note that repeat of the same chromosome locations shared by a set of pairs define a block of duplication.
Byrne,KP and Wolfe KH (2005), Table2 of supplementary information and Scerevisiae\_genome.tab file, chromosome location, from YGOB http://wolfe.gen.tcd.ie/ygob/ (last update 03/20/06)
Byrne KP, Wolfe KH. (2005) The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15(10):1456-61. PMID: 16169922
Loading required package: Category Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Loading required package: ScISI Loading required package: GO.db Loading required package: RpsiXML Loading required package: annotate Loading required package: XML Loading required package: graph Attaching package: 'graph' The following object is masked from 'package:XML': addNode Loading required package: RBGL Loading required package: hypergraph No methods found in package 'Biobase' for request: 'listlen' when loading 'RpsiXML' No methods found in package 'annotate' for requests: 'pubmed', 'buildPubMedAbst' when loading 'RpsiXML' Attaching package: 'RpsiXML' The following object is masked from 'package:IRanges': members Loading required package: apComplex Loading required package: SLGI Loading required package: lattice No methods found in package 'BiocGenerics' for request: 'plot' when loading 'SLGI' Loading required package: ppiStats Loading required package: ppiData KEGG.db contains mappings based on older data because the original resource was removed from the the public domain before the most recent update was produced. This package should now be considered deprecated and future versions of Bioconductor may not have it available. Users who want more current data are encouraged to look at the KEGGREST or reactome.db packages 'data.frame': 551 obs. of 5 variables: $ Gene1: chr "YIR018W" "YLR437C" "YOL091W" "YCR089W" ... $ Gene2: chr "YOL028C" "YML058W" "YBR148W" "YNR044W" ... $ Ka : num 2.26 2.14 2.08 1.57 1.57 ... $ ChrG1: chr "Chr9" "Chr12" "Chr15" "Chr3" ... $ ChrG2: chr "Chr15" "Chr13" "Chr2" "Chr14" ...
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