title: Removing intensity effects and identifying significant genes for Affymetrix arrays in macrophage migration inhibitory factor-suppressed neuroblastoma cells.
abstract: A semilinear in-slide model is introduced to remove the intensity effect in the scanning process. It is demonstrated that the intensity effect can be estimated accurately and removed effectively. This normalization step is vital for Affymetrix arrays to reveal relevant biological results when comparing gene expression in multiple arrays. The normalized expression ratios are analyzed further by a modified two-sample t test along with a sieved permutation scheme for computing P values. The improved specificity and sensitivity are demonstrated by using a study on the impact of macrophage migration inhibitory factor (MIF) reduction in neuroblastoma cells. With semilinear in-slide model analysis, expression of 166 genes was altered with a P value no greater than 0.001. Among those genes, 44 were altered >2-fold. MIF-regulated genes associated with tumor development including IL-8 and C-met, which are overexpressed in many tumors, were down-regulated in MIF-reduced cells. On the other hand, some tumor-suppressor genes such as EPHB6, visinin-like protein 1 (VSNL-1), and BLU were up-regulated in MIF-reduced cells. In addition, we demonstrated that down-regulation of MIF expression could result in a reduction in cell proliferation and tumor growth in vitro and in vivo. Our data not only demonstrate that targeting MIF expression is a promising therapeutic strategy in human neuroblastoma therapy but also indicate the MIF target genes for additional study.
authors.affiliation: Department of Operation Research and Financial Engineering, Princeton University, Princeton, NJ 08544, USA. jqfan@princeton.edu
authors.forename: Jianqing
authors.initials: J
authors.lastname: Fan
authors.forename: Yongxiong
authors.initials: Y
authors.lastname: Chen
authors.forename: Hiu Man
authors.initials: HM
authors.lastname: Chan
authors.forename: Paul K H
authors.initials: PK
authors.lastname: Tam
authors.forename: Yi
authors.initials: Y
authors.lastname: Ren
mesh_terms: D000818:Animals; D016375:Antisense Elements (Genetics); D045744:Cell Line, Tumor; D049109:Cell Proliferation; D015536:Down-Regulation / Q000187:drug effects / Q000235:genetics; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects*; D005822:Genetic Vectors / Q000235:genetics; D006801:Humans; D008263:Macrophage Migration-Inhibitory Factors / Q000494:pharmacology*; D051379:Mice; D008819:Mice, Nude; D009368:Neoplasm Transplantation; D009447:Neuroblastoma / Q000235:genetics* / Q000473:pathology; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015854:Up-Regulation / Q000187:drug effects / Q000235:genetics
chemical_list: D016375:Antisense Elements (Genetics); D008263:Macrophage Migration-Inhibitory Factors