The Multivariate Nonparametric Methods for Identifying Gene Sets with Differential Expression

• Published in: Gene Vol. 552; no. 1; pp. 18 - 23
• Main Authors: Khodakarim, Soheila, Tabatabaei, Seyyed Mohammad, AlaviMajd, Hamid
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 15.11.2014
• Subjects: Databases, Genetic; Gene Expression - genetics; Gene Expression Profiling - methods; Gene set analysis; Humans; Male; MMGSA; MRGSA; Multivariate Analysis; Oligonucleotide Array Sequence Analysis - methods; Phenotype; Prostatic Neoplasms - genetics; Abs-Cat; MRGSA; GSA; MMGSA; RMA; MRSGSA; Med-Cat; Gene set analysis; Rs-Cat
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2014.09.007

Gene Set Analysis (GSA) identifies differential expression gene sets amid the different phenotypes. The results of published papers in this filed are inconsistent and there is no consensus on the best method. In this paper two new methods, in comparison to the previous ones, are introduced for GSA. The MMGSA and MRGSA methods based on multivariate nonparametric techniques were presented. The implementation of five GSA methods (Hotelling's T2, Globaltest, Abs_Cat, Med_Cat and Rs_Cat) and the novel methods to detect differential gene expression between phenotypes were compared using simulated and real microarray data sets. In a real dataset, the results showed that the powers of MMGSA and MRGSA were as well as Globaltest and Tsai. The MRGSA method has not a good performance in the simulation dataset. The Globaltest method is the best method in the real or simulation datasets. The performance of MMGSA in simulation dataset is good in small-size gene sets. The GLS methods are not good in the simulated data, except the Med_Cat method in large-size gene sets. •The proposition of two nonparametric methods for gene set analysis (GSA)•Application of this method on the real data microarray set•Do simulation study for assessment of the novel methods and common GSA methods