title: Enhanced identification and biological validation of differential gene expression via Illumina whole-genome expression arrays through the use of the model-based background correction methodology.
abstract: Despite the tremendous growth of microarray usage in scientific studies, there is a lack of standards for background correction methodologies, especially in single-color microarray platforms. Traditional background subtraction methods often generate negative signals and thus cause large amounts of data loss. Hence, some researchers prefer to avoid background corrections, which typically result in the underestimation of differential expression. Here, by utilizing nonspecific negative control features integrated into Illumina whole genome expression arrays, we have developed a method of model-based background correction for BeadArrays (MBCB). We compared the MBCB with a method adapted from the Affymetrix robust multi-array analysis algorithm and with no background subtraction, using a mouse acute myeloid leukemia (AML) dataset. We demonstrated that differential expression ratios obtained by using the MBCB had the best correlation with quantitative RT-PCR. MBCB also achieved better sensitivity in detecting differentially expressed genes with biological significance. For example, we demonstrated that the differential regulation of Tnfr2, Ikk and NF-kappaB, the death receptor pathway, in the AML samples, could only be detected by using data after MBCB implementation. We conclude that MBCB is a robust background correction method that will lead to more precise determination of gene expression and better biological interpretation of Illumina BeadArray data.
authors.affiliation: Simmons Comprehensive Cancer Center Genomics Core Facility, Department of Radiation Oncology, Division of Molecular Radiation Biology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA.
authors.forename: Liang-Hao
authors.initials: LH
authors.lastname: Ding
authors.forename: Yang
authors.initials: Y
authors.lastname: Xie
authors.forename: Seongmi
authors.initials: S
authors.lastname: Park
authors.forename: Guanghua
authors.initials: G
authors.lastname: Xiao
authors.forename: Michael D
authors.initials: MD
authors.lastname: Story
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards; D015470:Leukemia, Myeloid, Acute / Q000235:genetics / Q000378:metabolism; D051379:Mice; D008808:Mice, Inbred CBA; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction / Q000235:genetics