Tuesday, April 26, 2016
(to read) Kaya, Ma, sanger strain lifespan study
Defining Molecular Basis for Longevity Traits in Natural Yeast Isolates
Alaattin Kaya1,#, Siming Ma1,#, Brian Wasko2, Mitchell Lee2, Matt Kaeberlein2, and Vadim N. Gladyshev1,*
1Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
RLS were provided
todo: download data, and Sanger resource data
Growth rates were determined using a Bioscreen C MBR machine by analysis of optical density in the OD420-580 range as previously described in combination with the YODA Software package18. The data on transcripts, peptides (proteins), metabolites and morphology were downloaded from Yeast Resource Center http://www.yeastrc.org/g2p/download.do. Values corresponding to the 22 strains were extracted; metabolite data were not available for 378604X. Metabolites with missing values in more than one strain (other than 378604X) were discarded; the remaining missing values (6 out of 107 metabolites) were imputed based on 10 nearest neighbors, using “knnImputation” function of R package “DMwR”. For comparison across the phenotypic data, the values were standardized across the strain by setting mean = 0 and standard deviation = 1. In addition, for genes represented by multiple peptides, we calculated the mean standardized values to perform the regression.