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September 3rd, 2010 | | Make me happy! One important task when analyzing microarray data is that of determining which genes changed their expressions significantly from one state to another, for example, from tissues in a cancerous state to tissues in a healthy state. In general, the procedure in which such a task is undertaken is known as gene filtering and has been extensively explored due to its potential for recognizing a reduced number of genes, which recognition can offer a shortcut to illness diagnosis, prognosis, and treatment (4-5, 7-21). Gene filtering has been explored through a variety of techniques based on normal distribution, such as the 2 sample t-test (17), ANOVA (22), and the Welch t-test (19), among others. Some authors stress the fact that gene expression data do not follow a normal distribution (18, 21, 23), proposing the use of nonparametric statistical tests such as the Mann-Whitney (MW) test (18), also known as the Wilcoxon test. Genes selected through a filtering procedure can be used for many purposes. Of particular interest to this study was defining a classifier to determine whether a given tissue belongs to a particular category (i.e. cancer or healthy) through measuring the relative expressions of the selected genes. Thus, the interest was on developing a cancer diagnosis that is based on classification. As a precedent, our research group has previously proposed a strategy (based on the Wilcoxon test) to carry out gene filtering and tissue classification (24-25), aiming first for simplicity rather than performance. In this study, using this initial strategy as a baseline, classification performance was targeted through the development of two new methods. The first method employed the Wilcoxon test for gene filtering and classification; however, this revised method introduced a gene-set selection step right after filtering to enhance classification performance. The second method capitalized on this new structure, and used the Nemenyi-Damico-Wolfe (NDW) multiple comparison nonparametric test as a distinctive enhancement strategy. For brevity, the descriptions of the Wilcoxon and the NDW tests have been omitted here but can be readily perused in a textbook on nonparametric statistical methods, such as that of Hollander and Wolfe (26). The structure of this paper is as follows: In the next section, microarray databases are described in general, along with the details of the proposed methods. The computational setting is then discussed in the ensuing section, followed by an assessment of the classification performance of the proposed methods vs. that of the baseline approach. Finally, conclusions are drawn and future plans are described.
In August 2004, the Law #230, approved by the Government of Puerto Rico in a three party resolution, created the University of Puerto Rico Comprehensive Cancer Center (UPRCCC), a public corporation affiliated to the University of Puerto Rico. This law established that this Center will be the organism responsible for executing the public policy related to the prevention, education, and research, as well as the clinical and treatment services related to cancer in Puerto Rico. The dual mission of the UPRCCC is: (1) To deliver the best research-driven cancer care through programs that integrate patient care, research, prevention, and education, and (2) To eradicate cancer in Puerto Rico using a multidisciplinary approach of basic, clinical, and population research. Thus, the UPRCCC is fundamental for the development of cancer control, research, and training efforts in Puerto Rico. More recently, in 2008, with funding from the Centers for Disease Control and Prevention, Puerto Rico published its first official Cancer Control Plan, a structured guide with measurable outcomes aimed at reducing the cancer burden in our population. All of the previously mentioned initiatives will continue to be key to the progress in cancer control and research in Puerto Rico and thus, to the quality of the preventive and treatment services that we will offer to our patients. The increase in the cancer burden in Puerto Rico has been accompanied by a substantial increase in the volume of published research and federal funds to academic institutions in Puerto Rico for cancer research. Despite this advancement, areas that need our continued support and development in the years to come include: 1) continued surveillance of cancer occurrence in Puerto Rico through the Puerto Rico Central Cancer Registry, 2) development of transdisciplinary and translational cancer research that encompass all areas of the cancer control continuum (prevention, early detection, diagnosis, treatment, survivorship), 3) outreach efforts that bring scientific knowledge to the development of targeted cancer control strategies for the community, 4) development of sound cancer-related public policy, and 5) continued training of the next generation of cancer researchers and health professionals. Our ability to collaborate in multidisciplinary local and international teams will be essential to our success. The forthcoming issue of the Puerto Rico Health Sciences Journal provides an informative summary of various research studies that are currently being conducted in Puerto Rico. The 17 articles in this issue describe diverse research areas in the cancer field including disease burden, disease prevention, correlates of cancer occurrence, diagnostic technologies and clinical management. In addition, an overview of cancer training efforts in the island is discussed. Our future as a healthy nation will require a concerted effort between government, academia and industry that lead the research, training, and public policy efforts that will ultimately result in improved cancer prevention and control outcomes for the people of Puerto Rico. We hope you find in this edition of the journal a well-rounded overview of cancer research in Puerto Rico.
The main goal of the Training Program is to increase the number of Hispanic students knowledgeable and committed to careers in cancer research and cancer medicine. The specific objectives are to prepare Hispanic students to pursue careers in cancer research, cancer medicine, and population sciences and to establish a Career Development Program for clinical and basic scientist faculty at the Comprehensive Cancer Center of the University of Puerto Rico (UPRCCC). The Training Program includes a series of didactic and research experiences, and enrichment activities that include on-campus cancer research at the UPR campuses during the academic year, and summer research and year-round rotations to MDACC. These experiences are complemented and supported by a structured Mentoring Program for students and junior investigators. The mentors are well recognized senior Faculty, mostly from MDACC. Training Opportunities Various research programs are available in UPR and MDACC, all sponsored by the U54 Training Program. In the UPR there is Research Assistantships Stipends Program for Undergraduate and Graduate Students. Students have the opportunity of working in cancer research projects under the guidance of Faculty in mid to senior stages of their academic careers. Most of these scientists are re-gearing their careers to Cancer Research. The students are also required to attend Seminars and Workshops offered through the academic year, mostly offered by visiting world-renowned scientists.