Enhancing the usability and performance of structured association mapping algorithms using automation, parallelization, and visualization in the GenAMap software system

BMC Genetics

Volumn 13, Issue , 2012, Pages

  Curtis, Ross E ^a,b   Goyal, Anuj ^b   Xing, Eric P ^b  

^a CARNEGIE MELLON UNIVERSITY   (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; AUTOMATION; COMPUTER PROGRAM; GENE MAPPING; GENETIC ASSOCIATION; INTERNET;

ALGORITHMS; AUTOMATION; CHROMOSOME MAPPING; GENETIC ASSOCIATION STUDIES; SOFTWARE;

EID: 84859185929     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-13-24     Document Type: Article

References (30)

1. Schadt EE. Molecular networks as sensors and drivers of common human diseases. Nature 2009, 461:218-223. 10.1038/nature08454, 19741703.
2. Gilad Y, Rifkin SA, Pritchard JK. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet 2008, 24(8):408-45. 10.1016/j.tig.2008.06.001, 2583071, 18597885.
3. Simpson MA, Irving MD, Asilmax E, Gray MJ, Dafou D, Elmslie FV, Mansour S, Holder SE, Brain CE, Burton BK, Kim KH, Pauli RM, Aftimos S, Stewart H, Kim CA, Holder-Espinasse M, Robertson SP, Drake WM, Trembath RC. Mutations in NOTCH2 cause Hajdu-Cheney syndrome, a disorder of severe and progressive bone loss. Nat Genet 2011, 43:303-305. 10.1038/ng.779, 21378985.
4. Wang F, Xu CQ, He Q, Cai JP, Li XC, Wang D, Xiong X, Liao YH, Zeng QT, Yang YZ, Cheng X, Yang R, Wang CC, Wu G, Lu QL, Bai Y, Huang YF, Yin D, Yang Q, Wang XJ, Dai DP, Zhang RF, Wan J, Ren JH, Li SS, Zhao YY, Fu FF, Huang Y, Li QX, Shi SW, et al. Genome-wide association identifies a susceptibility locus for coronary artery disease in the Chinese Han population. Nat Genet 2011, 43:345-349. 10.1038/ng.783, 21378986.
5. Manolio RA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler E, Gibson G, Haines JL, Mackay TFC, McCarroll SA, Visscher PM. Finding the missing heritability of complex disease. Nature 2009, 461:747-753. 10.1038/nature08494, 2831613, 19812666.
6. Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, Avila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich R. Mapping the genetic architecture of gene expression in human liver. PLoS Biol 2008, 6(5):e107. 10.1371/journal.pbio.0060107, 2365981, 18462017.
7. Cookson W, Liang L, Abecasis G, Moffatt M, Lanthrop M. Mapping complex disease traits with global gene expression. Nat Rev Genet 2009, 10:184-194. 10.1038/nrg2537, 19223927.
8. Zhu J, Zhang B, Smith EN, Drees B, Brem RB, Kruglyak L, Bumgarner RE, Schadt EE. Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet 2008, 40(7):854-861. 10.1038/ng.167, 2573859, 18552845.
9. Kim S, Xing EP. Statistical estimation of correlated genome associations to a quantitative trait network. PLoS Genet 2009, 5(8):e1000587. 10.1371/journal.pgen.1000587, 2719086, 19680538.
10. Kim S, Xing EP. Tree-guided group lasso for multi-task regression with structured sparsity. Proceedings of the 27th International Conference on Machine Learning (ICML) 2010,
11. Puniyani K, Kim S, Xing EP. Multi-population GWA mapping via multi-taks regularized regression. Bioinformatics 2010, 26(12):i208-i216. 10.1093/bioinformatics/btq191, 2881376, 20529908.
12. Lee S, Zhu J, Xing EP. Adaptive multi-task Lasso: with application to eQTL detection. Advances in Neural Information Processing Systems 23 (NIPS) 2010,
13. Chen X, Kim S, Lin Q, Carbonell JG, Xing EP. Graph-structured multi-task regression and an efficient optimization method for general fused Lasso. CoRR 2010,
14. Curtis RE, Yin J, Kinnaird P, Xing EP. Finding genome-transcriptome-phenome associations with structured association mapping and visualization in GenAMap. Pac Symp Biocomput 2012,
15. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Skalr P, de Bakker PIW, Daly MF, Sham PC. PLINK: a toolset for whole-gehome association and population-based linkage analysis. Am J Human Genet 2007, 81(3):559-575.
16. Friedman J, Hastie T, Tibshirani R. Regularization paths for generalized linear models via coordinate descent. J Stat Softw 2010, 33(1):1-22. 2929880, 20808728.
17. Curtis RE, Wenzel S, Myers DA, Bleecker E, Xing EP. Population analysis of asthma genome-wide association data using GenAMap. Presented at the 61st Annual Meeting of the American Society of Human Genetics 2011,
18. Friedman J, Hastie T, Tibshirani R. Sparse inverse covariance estimation with the graphical lasso. Biostatistics 2007, 9(3):432-441. 10.1093/biostatistics/kxm045, 3019769,3019769, 18079126.
19. Zhang B, Horvath S. A general framework for weighted gene co-expression newtork analysis. Stat Appl Genet Molec Biol 2005, 4(1):Article 17.
20. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000, 155:945-959. 1461096, 10835412.
21. Curtis RE, Xing EP. GenAMap: an integrated analytic and visualization platform for GWA and eQTL analysis. Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology (ISMB); Technology Track 2010,
22. Curtis RE, Kinnaird P, Xing EP. GenAMap: visualization strategies for association mapping. IEEE Symp Biol Data Vis 2011, 1:87-95.
23. R Development Core Team R Foundation for Staistical Computing. R Development Core Team., http://www.R-project.org
24. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettlin M, Dudoit S, Ellis B, Gautier L, Ge Y. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
25. Thain D, Tannenbaum T, Livny M. Distributed computing in practice: the Condor experience. Concurrency Pract Ex 2005, 17(2-4):323-356.
26. The UniProt Consortium Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 2011, 39:D214-D219. 3013648, 21051339, The UniProt Consortium.
27. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001, 29(1):308-311. 10.1093/nar/29.1.308, 29783, 11125122.
28. Brem RB, Kruglyak L. The landscape of genetic complexity across 5700 gene expression traits in yeast. Proc Natl Acad Sci USA 2005, 102(5):1572-1577. 10.1073/pnas.0408709102, 547855, 15659551.
29. Johannesson M, Lopez-Aumatell R, Stridh P, Diez M, Tuncel J, Blazquez G, Martinez-Membrives E, Canete T, Vicens-Costa E, Graham D, Copley RR, Hernandez-Pliego P, Beyeen AD, Ockinger J, Fernandez-Santamaria C, Gulko PS, Brenner M, Tobena A, Guitart-Masip M, Gimenez-Llort L, Dominiczak A, Holmdahl R, Gauguier D, Olsson T, Mott R, Valdar W, Redei EE, Fernandez-Teruel A, Flint J. A resource for the simultaneous high-resolution mapping of multiple quantitative trait loci in rats: the NIH heterogeneous stock. Genome Res 2009, 19(1):150-158. 2612958, 18971309.
30. Chen WY, Song Y, Bai H, Lin CJ, Chang EY. Parallel spectral clustering in distributed systems. IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI) 2010, 33(3)., http://www.cs.ucsb.edu/~wychen/sc