Comparison of Profile Similarity Measures for Genetic Interaction Networks

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Deshpande, Raamesh ^a   VanderSluis, Benjamin ^a   Myers, Chad L ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DATA PROCESSING; GENE IDENTIFICATION; GENE INTERACTION; GENETIC INTERACTION NETWORK; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE;

COMPUTATIONAL BIOLOGY; EPISTASIS, GENETIC; GENE EXPRESSION REGULATION, FUNGAL; GENE REGULATORY NETWORKS; GENES, FUNGAL; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES; TRANSCRIPTOME;

EID: 84880021782     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0068664     Document Type: Article

References (36)

1. Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, et al. (2010) The genetic landscape of a cell. Science 327: 425-431.
2. Bellay J, Atluri G, Sing TL, Toufighi K, Costanzo M, et al. (2011) Putting genetic interactions in context through a global modular decomposition. Genome Res 21: 1375-1387.
3. Avery L, Wasserman S, (1992) Ordering gene function: the interpretation of epistasis in regulatory hierarchies. Trends Genet 8: 312-316.
4. Mani R, St Onge RP, Hartman JLt, Giaever G, Roth FP, (2008) Defining genetic interaction. Proc Natl Acad Sci U S A 105: 3461-3466.
5. Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, et al. (2010) Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods 7: 1017-1024.
6. Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, et al. (2007) Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446: 806-810.
7. Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, et al. (2008) Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science 322: 405-410.
8. Dixon SJ, Fedyshyn Y, Koh JL, Prasad TS, Chahwan C, et al. (2008) Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. Proc Natl Acad Sci U S A 105: 16653-16658.
9. Ryan CJ, Roguev A, Patrick K, Xu J, Jahari H, et al. (2012) Hierarchical Modularity and the Evolution of Genetic Interactomes across Species. Mol Cell 46: 691-704.
10. Typas A, Nichols RJ, Siegele DA, Shales M, Collins SR, et al. (2008) High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods 5: 781-787.
11. Boutros M, Kiger AA, Armknecht S, Kerr K, Hild M, et al. (2004) Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 303: 832-835.
12. Lehner B, Crombie C, Tischler J, Fortunato A, Fraser AG, (2006) Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways. Nat Genet 38: 896-903.
13. Barbie DA, Tamayo P, Boehm JS, Kim SY, Moody SE, et al. (2009) Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature 462: 108-112.
14. Falkowski BJ, (1998) On certain generalizations of inner product similarity measures. Journal of the American Society for Information Science 49: 854-858.
15. Wang ZW, Wong SKM, Yao YY (1992) An analysis of vector space models based on computational geometry. Proceeding SIGIR '92 Proceedings of the 15th annual international ACM SIGIR conference on Research and development in information retrieval.
16. Leydesdorff L, (2008) On the normalization and visualization of author co-citation data: Salton's Cosine versus the Jaccard index. Journal of the American Society for Information Science & Technology 59: 77-85.
17. Egghe L, Leydesdorff L, (2009) The relation between Pearson's correlation coefficient r and Salton's cosine measure. Journal of the American Society for Information Science & Technology 60: 1027-1036.
18. Adler J, Parmryd I, (2010) Quantifying colocalization by correlation: the Pearson correlation coefficient is superior to the Mander's overlap coefficient. Cytometry A 77: 733-742.
19. Haranczyk M, Holliday J, (2008) Comparison of similarity coefficients for clustering and compound selection. J Chem Inf Model 48: 498-508.
20. Yona G, Dirks W, Rahman S, Lin DM, (2006) Effective similarity measures for expression profiles. Bioinformatics 22: 1616-1622.
21. Dalirsefat SB, da Silva Meyer A, Mirhoseini SZ, (2009) Comparison of similarity coefficients used for cluster analysis with amplified fragment length polymorphism markers in the silkworm, Bombyx mori. J Insect Sci 9: 1-8.
22. Obayashi T, Kinoshita K, (2009) Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression. DNA Research 16: 249-260.
23. Leiserson MD, Tatar D, Cowen LJ, Hescott BJ, (2011) Inferring mechanisms of compensation from E-MAP and SGA data using local search algorithms for max cut. J Comput Biol 18: 1399-1409.
24. Collins SR, Schuldiner M, Krogan NJ, Weissman JS, (2006) A strategy for extracting and analyzing large-scale quantitative epistatic interaction data. Genome Biol 7: R63.
25. Reshef DN, Reshef YA, Finucane HK, Grossman SR, McVean G, et al. (2011) Detecting novel associations in large data sets. Science 334: 1518-1524.
26. Gillis J, Pavlidis P, (2011) The impact of multifunctional genes on "guilt by association" analysis. PLoS One 6: e17258.
27. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
28. Myers CL, Barrett DR, Hibbs MA, Huttenhower C, Troyanskaya OG, (2006) Finding function: evaluation methods for functional genomic data. BMC Genomics 7: 187.
29. Pearson K, (1920) Notes on the History of Correlation. Biometrika 13: 25-45.
30. Schechtman E, Yitzhaki S, (1999) On the proper bounds of the Gini correlation. Economics Letters 63: 133-138.
31. Parsons AB, Brost RL, Ding H, Li Z, Zhang C, et al. (2004) Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat Biotechnol 22: 62-69.
32. de Hoon MJ, Imoto S, Nolan J, Miyano S, (2004) Open source clustering software. Bioinformatics 20: 1453-1454.
33. Page RDM, (1996) Tree View: An application to display phylogenetic trees on personal computers. Computer applications in the biosciences: CABIOS 12: 357-358.
34. Spearman C, (1904) The proof and measurement of association between two things. American Journal of Psychology 15: 72-101.
35. Russell PF, Rao TR, (1940) On habitat and association of species of anopheline larvae in south-eastern Madras. Journal of Malaria Institute India 3: 25.
36. P J (1901) Étude comparative de la distribuition florale dans une portion des Alpes et des Jura. Bull Soc Vandoise Sci Nat 37.