Bactome III: OLIgonucleotide Variable Expression Ranker (OLIVER) 1.0, Tool for Identifying Suitable Reference (Invariant) Genes from Large Microarray Datasets

Oliver YW Chan, Bryan MH Keng, Maurice HT Ling

Abstract


Reference genes are crucial in gene expression analysis where varying gene expressions are reported as changes with respect to the expression of reference genes. Hence, reference genes are assumed to be stably expressed under most circumstances. Previous studies have shown that common algorithms for identifying of potential reference genes are not suitable for large microarray-sized datasets. Our previous work had derived methods for identification of reference genes from large microarray-sized datasets and the performances of these methods are linear to sample size. These methods had been implemented as a tool, OLIgonucleotide Variable Expression Ranker (OLIVER), which can be downloaded from http://sourceforge. net/projects/bactome/files/OLIVER/OLIVER_1.zip. This manuscript documents the implementation of OLIVER, which had been incorporated as part of Bactome project (http://www.sf.net/projects/bactome). These codes are licensed under GNU General Public License version 3 for academic and non-for-profit use.