YEASTOHNOLOG: List of ohnolog gene pairs from Byrne, K.P and Wolfe, K.H...

In PCpheno: Phenotypes and cellular organizational units

Description

List of 551 paralogous Saccharomyces cerevisiae gene pairs formed by Whole Genome Duplication (WGD) or ohnolog pairs.

Usage

data(YEASTOHNOLOG)

Format

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.

Details

Gene1 Gene2

Systematic gene names of the ohnolog pairs

Ka

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.

ChrG1 ChrG2

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.

Author(s)

N. LeMeur

Source

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)

References

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

Examples

data(YEASTOHNOLOG)
str(YEASTOHNOLOG)

Example output

Loading required package: Category
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    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

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Welcome to Bioconductor

    Vignettes contain introductory material; view with
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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" ...

PCpheno documentation built on Nov. 8, 2020, 5:10 p.m.