KruX: Matrix-based non-parametric eQTL discovery

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Qi, Jianlong ^a,b   Asl, Hassan F ^c   Björkegren, Johan ^c,d   Michoel, Tom ^a,e  

^a UNIVERSITY OF FREIBURG   (Germany)

^b MCGILL UNIVERSITY   (Canada)

^c KAROLINSKA INSTITUTE   (Sweden)

^d UNIVERSITY OF TARTU   (Estonia)

^e UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

eQTL; Matrix algebra; Non parametric methods; Software

Indexed keywords

EQTL; HIGH-PERFORMANCE COMPUTING; HUMAN BLOOD SAMPLES; KRUSKAL-WALLIS TESTS; MATRIX MULTIPLICATION; NON-PARAMETRIC STATISTICAL TESTS; NONPARAMETRIC METHODS; QUANTITATIVE TRAIT LOCUS;

COMPUTER SOFTWARE; MATLAB; MATRIX ALGEBRA; STATISTICS;

STATISTICAL TESTS;

ALGORITHM; ARTICLE; BIOLOGY; COMPUTER PROGRAM; GENETICS; GENOME; GENOTYPE; HUMAN; METHODOLOGY; NONPARAMETRIC TEST; QUANTITATIVE TRAIT LOCUS; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENOME; GENOTYPE; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; REPRODUCIBILITY OF RESULTS; SOFTWARE; STATISTICS, NONPARAMETRIC;

EID: 84892429869     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-11     Document Type: Article

References (13)

1. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Nat Acad Sci 2009, 106(23):9362-9367. 10.1073/pnas.0903103106, 2687147, 19474294.
2. Schadt EE. Molecular networks as sensors and drivers of common human diseases. Nature 2009, 461:218-223. 10.1038/nature08454, 19741703.
3. Cookson W, Liang L, Abecasis G, Moffatt M, Lathrop M. Mapping complex disease traits with global gene expression. Nat Rev Genet 2009, 10(3):184-194. 10.1038/nrg2537, 19223927.
4. Foss EJ, Radulovic D, Shaffer SA, Ruderfer DM, Bedalov A, Goodlett DR, Kruglyak L. Gentic basis of proteome variation in yeast. Nat Genet 2007, 39:1369-1375. 10.1038/ng.2007.22, 17952072.
5. Nicholson G, Rantalainen M, Li JV, Maher AD, Malmodin D, Ahmadi KR, Faber JH, Barrett A, Min JL, Rayner NW, et al. A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. PLoS Genetics 2011, 7(9):1002270.
6. Shabalin AA. Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics 2012, 28(10):1353-1358. 10.1093/bioinformatics/bts163, 3348564, 22492648.
7. Kruglyak L, Lander ES. A nonparametric approach for mapping quantitative trait loci. Genetics 1995, 139(3):1421-1428. 1206467, 7768449.
8. 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, et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol 2088, 6:107.
9. Kruskal WH, Wallis WA. Use of ranks in one-criterion variance analysis. J Am Stat Assoc 1952, 47(260):583-621.
10. Leek JT, Storey JD. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet 2007, 3(9):161.
11. Listgarten J, Kadie C, Schadt EE, Heckerman D. Correction for hidden confounders in the genetic analysis of gene expression. Proc Nat Acad Sci 1646, 107(38):5-16470.
12. Brem RB, Kruglyak L. The landscape of genetic complexity across 5,700 gene expression traits in yeast. PNAS 2005, 102(5):1572-1577. 10.1073/pnas.0408709102, 547855, 15659551.
13. Hägg S, Skogsberg J, Lundström J, Noori P, Nilsson R, Zhong H, Maleki S, Shang MM, Brinne B, Bradshaw M, Bajic VB, Samnegard A, Silveira A, Kaplan LM, Gigante B, Leander K, de Faire U, Rosfors S, Lockowandt U, Liska J, Konrad P, Takolander R, Franco-Cereceda A, Schadt EE, Ivert T, Hamsten A, Tegner J, Björkegren J. Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm atherosclerosis gene expression (STAGE) study. PLoS Genet 1000754, 5(12).