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Gene set analysis: limitations in popular existing methods and proposed improvements


, : Gene set analysis: limitations in popular existing methods and proposed improvements. Bioinformatics 30(19): 2747-2756

Gene set analysis is the analysis of a set of genes that collectively contribute to a biological process. Most popular gene set analysis methods are based on empirical P-value that requires large number of permutations. Despite numerous gene set analysis methods developed in the past decade, the most popular methods still suffer from serious limitations. We present a gene set analysis method (mGSZ) based on Gene Set Z-scoring function (GSZ) and asymptotic P-values. Asymptotic P-value calculation requires fewer permutations, and thus speeds up the gene set analysis process. We compare the GSZ-scoring function with seven popular gene set scoring functions and show that GSZ stands out as the best scoring function. In addition, we show improved performance of the GSA method when the max-mean statistics is replaced by the GSZ scoring function. We demonstrate the importance of both gene and sample permutations by showing the consequences in the absence of one or the other. A comparison of asymptotic and empirical methods of P-value estimation demonstrates a clear advantage of asymptotic P-value over empirical P-value. We show that mGSZ outperforms the state-of-the-art methods based on two different evaluations. We compared mGSZ results with permutation and rotation tests and show that rotation does not improve our asymptotic P-values. We also propose well-known asymptotic distribution models for three of the compared methods. mGSZ is available as R package from cran.r-project.org.

US$19.90

PMID: 24903419

DOI: 10.1093/bioinformatics/btu374


Other references

Gutierrez Aquilar, Rafael, 1992: Neurobiology of opioids. Ciencia (Mexico City) 43(1): 47-61

Halsey J.F.; Harris M.; Hale R., 1986: Use of an immunoglobulin g radioallergosorbent assay to measure patient responses to heat denatured antigen. Annals of Allergy 56(6): 531

Walker, L.M., 1992: How to tell if an HMO will make you money. Medical Economics 69(22): 161-2, 165, 168 Passim

Anonymous, 1986: Payment by results to encourage better output. A system of price bonuses is being introduced to the USSR to encourage the sale of grain. Producers who fail to achieve current plan targets will qualify for a 50% bonus on all grain supplied above the 1981-85 annual average. Those who fulfil the...

Foster C.S.; Tolchin N.; Opremcak E.M., 1987: Cholera toxin induces while carbamylcholine decreases hsv 1 viral reactivation in latently infected murine trigeminal ganglia in vitro. Investigative Ophthalmology & Visual Science 28(3 SUPPL): 367

Gottlob, R., 1972: Changes in the venous valves following spontaneous thrombolysis. International Surgery 57(9): 738-739

Vasylevs'kyy, S.I.; Senchyk, G.A.; Lysenko, A.B.; Rusanov, E.B.; Chernega, A.N.; Jezierska, J.; Krautscheid, H.; Domasevitch, K.V.; Ozarowski, A., 2014: 1,2,4-Triazolyl-carboxylate-based MOFs incorporating triangular Cu(II)-hydroxo clusters: topological metamorphosis and magnetism. Bifunctional 1,2,4-triazole-carboxylate ligands, an achiral 1,2,4-triazol-4-yl-acetic acid (trgly-H) and a chiral (d)-2-(1,2,4-triazol-4-yl)-propionic acid (d-trala-H), derived from the corresponding α-amino acid precursors revealed unique bindin...

Mathison, Y.; Acuna, Y.; Campos, H.; Israel, A., 1996: Role of histamine H-3 receptor on the cardiovascular response to footshock. Journal of Physiology (Cambridge) 493P(0): 83S

Martin-Schild, S., 2012: tPA for stroke--are we ready to remove the barriers?. European Journal of Neurology 19(3): 359-359

Lowe J.B.; Mcquillan J.J.; Sacchettini J.A.; Gordon J.I., 1986: Rat liver and intestinal fatty acid binding proteins synthesized in escherichia coli exhibit differences in ligand affinity and stoichiometry. American Heart Association Monograph (124): II-322