Friday, January 2, 2015

He 14, ibuprofen on RLS

He C, Tsuchiyama SK, Nguyen QT, Plyusnina EN, Terrill SR, et al. (2014) Enhanced Longevity by Ibuprofen, Conserved in Multiple Species, Occurs in Yeast through Inhibition of Tryptophan Import. PLoS Genet 10(12): e1004860. doi:10.1371/journal.pgen.1004860

He14 partitioned the yeast genes into LL long-lived and NLL (non LL). This partition can be used to verify my svm project.  There were 137 LL genes and 3840 non-LL genes. 

0.2mM ibuprofen was used for yeast cells (a bit too high?)

Used Giaever's drug screen to identify the tryptophas pathway in ibuprofen effect. 

Did miscropscopic screen on bud sizes and growth. This is an useful data resource.

tb = read.xlsx("journal.pgen.1004860.s010.xlsx", 1)
tb = tb[,1:6]; tb[,1] = as.character(tb[,1])
names(tb)= c("ORF","RLS","BirthSize","MeanSize","G1DNAcontent", "Fitness")

#Birthsize is from
Hoose SA, Rawlings JA, Kelly MM, Leitch MC, Ababneh QO, et al. (2012) A
systematic analysis of cell cycle regulators in yeast reveals that most factors act
independently of cell size to control initiation of division. PLoS Genet 8:

Truong SK, McCormick RF, Polymenis M (2013) Genetic Determinants of Cell
Size at Birth and Their Impact on Cell Cycle Progression in Saccharomyces
cerevisiae. G3 (Bethesda) 3: 1525–1530.

# Fitness is from Giaever2002Nature,

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