Dataset Information

GPS-MBA: computational analysis of MHC class II epitopes in type 1 diabetes.

ABSTRACT: As a severe chronic metabolic disease and autoimmune disorder, type 1 diabetes (T1D) affects millions of people world-wide. Recent advances in antigen-based immunotherapy have provided a great opportunity for further treating T1D with a high degree of selectivity. It is reported that MHC class II I-A(g7) in the non-obese diabetic (NOD) mouse and human HLA-DQ8 are strongly linked to susceptibility to T1D. Thus, the identification of new I-A(g7) and HLA-DQ8 epitopes would be of great help to further experimental and biomedical manipulation efforts. In this study, a novel GPS-MBA (MHC Binding Analyzer) software package was developed for the prediction of I-A(g7) and HLA-DQ8 epitopes. Using experimentally identified epitopes as the training data sets, a previously developed GPS (Group-based Prediction System) algorithm was adopted and improved. By extensive evaluation and comparison, the GPS-MBA performance was found to be much better than other tools of this type. With this powerful tool, we predicted a number of potentially new I-A(g7) and HLA-DQ8 epitopes. Furthermore, we designed a T1D epitope database (TEDB) for all of the experimentally identified and predicted T1D-associated epitopes. Taken together, this computational prediction result and analysis provides a starting point for further experimental considerations, and GPS-MBA is demonstrated to be a useful tool for generating starting information for experimentalists. The GPS-MBA is freely accessible for academic researchers at: http://mba.biocuckoo.org.

SUBMITTER: Cai R

PROVIDER: S-EPMC3313963 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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GPS-MBA: computational analysis of MHC class II epitopes in type 1 diabetes.

Cai Ruikun R Liu Zexian Z Ren Jian J Ma Chuang C Gao Tianshun T Zhou Yanhong Y Yang Qing Q Xue Yu Y

PloS one 20120327 3

As a severe chronic metabolic disease and autoimmune disorder, type 1 diabetes (T1D) affects millions of people world-wide. Recent advances in antigen-based immunotherapy have provided a great opportunity for further treating T1D with a high degree of selectivity. It is reported that MHC class II I-A(g7) in the non-obese diabetic (NOD) mouse and human HLA-DQ8 are strongly linked to susceptibility to T1D. Thus, the identification of new I-A(g7) and HLA-DQ8 epitopes would be of great help to furth ...[more]

PMID: 22479466

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Dataset Information

GPS-MBA: computational analysis of MHC class II epitopes in type 1 diabetes.

Publications

GPS-MBA: computational analysis of MHC class II epitopes in type 1 diabetes.

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