Balony: A software package for analysis of data generated by synthetic genetic array experiments

BMC Bioinformatics

Volumn 14, Issue 1, 2013, Pages

  Young, Barry P ^a   Loewen, Christopher J R ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Array; Image analysis; Software; Yeast

Indexed keywords

ARRAY; BIOLOGICAL INSIGHT; FREELY AVAILABLE SOFTWARE; GENETIC INTERACTION; HIGH-THROUGHPUT SCREENS; QUANTITATIVE DATA; REPRODUCIBILITIES; YEAST SACCHAROMYCES CEREVISIAE;

COMPUTER SOFTWARE; EXPERIMENTS; GENES; IMAGE ANALYSIS;

YEAST;

SACCHAROMYCES CEREVISIAE;

FUNGAL PROTEIN;

BACTERIAL COUNT; BIOSYNTHESIS; COMPUTER INTERFACE; COMPUTER PROGRAM; CYTOLOGY; DEVICES; DNA MICROARRAY; FUNGAL GENE; GENETIC ASSOCIATION; GENETICS; HIGH THROUGHPUT SCREENING; IMAGE PROCESSING; INTERNET; ISOLATION AND PURIFICATION; MUTATION; PROCEDURES; SACCHAROMYCES CEREVISIAE; TRENDS; ARTICLE; EQUIPMENT; METHODOLOGY;

COLONY COUNT, MICROBIAL; FUNGAL PROTEINS; GENES, FUNGAL; GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT SCREENING ASSAYS; IMAGE PROCESSING, COMPUTER-ASSISTED; INTERNET; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SACCHAROMYCES CEREVISIAE; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84888773226     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-354     Document Type: Article

References (13)

1. Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 2001, 294(5550):2364-2368. 10.1126/science.1065810, 11743205.
2. Tong AH, Boone C. Synthetic genetic array analysis in Saccharomyces cerevisiae. Methods Mol Biol 2006, 313:171-192.
3. Dittmar JC, Reid RJ, Rothstein R. ScreenMill: a freely available software suite for growth measurement, analysis and visualization of high-throughput screen data. BMC Bioinforma 2010, 11:353.
4. Wagih O, Usaj M, Baryshnikova A, Vandersluis B, Kuzmin E, Costanzo M, Myers CL, Andrews BJ, Boone CM, Parts L. SGAtools: one-stop analysis and visualization of array-based genetic interaction screens. Nucleic Acids Res 2013, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692131/.
5. Rasband WS. ImageJ, U S National Institutes of Health Bethesda Maryland, USA, http://imagej.nih.gov/ij/ 1997-2011.
6. Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, et al. SGD: Saccharomyces Genome Database. Nucleic Acids Res 1998, 26(1):73-79. 10.1093/nar/26.1.73, 147204, 9399804.
7. Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, et al. The genetic landscape of a cell. Science 2010, 327(5964):425-431. 10.1126/science.1180823, 20093466.
8. Jorgensen P, Nelson B, Robinson MD, Chen Y, Andrews B, Tyers M, Boone C. High-resolution genetic mapping with ordered arrays of Saccharomyces cerevisiae deletion mutants. Genetics 2002, 162(3):1091-1099. 1462329, 12454058.
9. Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, et al. Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nature methods 2010, 7(12):1017-1024. 10.1038/nmeth.1534, 3117325, 21076421.
10. Collins SR, Schuldiner M, Krogan NJ, Weissman JS. A strategy for extracting and analyzing large-scale quantitative epistatic interaction data. Genome Biol 2006, 7(7):R63. 10.1186/gb-2006-7-7-r63, 1779568, 16859555.
11. Cleveland WS. Robust locally weighted regression and smoothing scatterplots. J Am Stat Assoc 1979, 74(368):829-836.
12. Baldi P, Long AD. A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics 2001, 17(6):509-519. 10.1093/bioinformatics/17.6.509, 11395427.
13. Boone C, Bussey H, Andrews BJ. Exploring genetic interactions and networks with yeast. Nature Rev Genet 2007, 8(6):437-449. 10.1038/nrg2085, 17510664.