It is well known that cancer progression is fueled by genetic aberrations, disrupting various important cellular machineries and some types of chromosomal aberrations are quite recurrently observed in some cancers, indicating an important (possibly causative) relationship between those aberrations and cancer progression. Therefore, the analysis of DNA microarrays based on recurrent genetic aberrations as a prognostic factor can give an important insight into neoplasmic progression in those types of cancers. This also entails recruitment of more sequence-specific information and chromosomal location of probes in analyzing related microarray data. In Waldenstrom macroglobulinemia (WM), a lymphoid neoplasm associated with accumulation of lymphoplasmacytic cells in bone marrow and an elevated monoclonal IgM in serum, chromosome 6 long arm abnormalities (?6) are observed quite recurrently. We present the analysis result of a gene expression data set, obtained from 24 WM patients using ?6 as an indicative prognostic factor. The set of genes showing differential expression between 6q normal and deletion groups were identified and their biological annotations based on Gene Ontology were investigated. We found that ?6 affected many biological processes and was associated with transcriptional up-regulation of downstream genetic cascades, which likely indicates release of regulatory control by some tumor suppressor genes.