Prediction of operator-binding protein by discriminant analysis |
| |
| Institution: | 1. Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA;2. Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile;3. Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA;4. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA;5. Department of Engineering, Texas Southern University, Houston, TX, USA;6. Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA;7. McCombs Institute for the Early Detection and Treatment of Cancer, The University of Texas MD Anderson Cancer Center, Houston, TX, USA;8. Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA;9. Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel;10. Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA;11. Departments of Medicine, Oncology and Molecular Microbiology & Immunology, Johns Hopkins University School of Medicine and the Bloomberg School of Public Health, Baltimore, MD, USA;12. Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA;13. Department of Pathology and The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA;14. Sheikh Ahmed Pancreatic Cancer Research Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA;15. Resphera Biosciences, Baltimore, MD, USA;16. Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA;17. Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA;1. Mucosal Immunology Laboratory, Department of Convergence Medicine, University of Ulsan College of Medicine/Asan Medical Center, Seoul, Republic of Korea;2. Asan Institute for Life Science, Asan Medical Center, Seoul, Republic of Korea;3. Department of Gastroenterology, Asan Medical Center, Seoul, Republic of Korea;4. Academy of Immunology and Microbiology, Institute for Basic Science, Pohang, Republic of Korea;5. National Center for Agricultural Utilization Research, USDA ARS, Peoria, IL, USA;6. Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA;7. Department of Biological Sciences, Rutgers University, Newark, NJ, USA;1. Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA;2. Department of Bioengineering, Stanford University, Stanford, CA 94305, USA;3. Department of Genetics, Stanford University, Stanford, CA 94305, USA;4. Department of CHEM-H, Stanford University, Stanford, CA 94305, USA;5. Department of Comparative Medicine, Stanford University, Stanford, CA 94305, USA;6. Department of Medicine, Stanford University, Stanford, CA 94305 USA;7. Chan Zuckerberg Biohub, San Francisco, CA 94158 USA;1. Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China;2. Department of Preventive Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China;3. Department of Veterinary Medicine, Faculty of Veterinary Science, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan;1. College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China;2. School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China;3. Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei 230009, China;4. State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China |
| |
| Abstract: | A number of operator-binding proteins contain similar sequence features to Cro and cI repressors of bacteriophage and CAP protein of Escherichia coli, such as conserved amino acids at constant positions. However, these sequence patterns also occur in proteins that are not operator-binding. We use sequence analogy information in conjunction with a pattern recognition algorithm. The functional and structural properties, e.g., distributions of hydrophobicity, hydrophilicity, charged amino acids, electrostatic free energy, and helical structures of protein are also considered. Within the framework of discriminant analysis, we calculate the above variables and search for a better combination of variables. To assess the discriminatory power of these variables, we allocated additional sequences and predict DNA-binding regions of regulatory proteins not included in the training set. |
| |
| Keywords: | |
| 本文献已被 ScienceDirect 等数据库收录！ |
|
