Lv Hongqiang, Han Jiuqiang, Liu Jun, Zheng Jiguang, Zhong Dexing, Liu Ruiling
School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, PR China.
School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, PR China.
J Theor Biol. 2014 Nov 7;360:78-82. doi: 10.1016/j.jtbi.2014.06.033. Epub 2014 Jul 5.
Immunosuppressive domain (ISD) is a conserved region of transmembrane proteins (TM) in envelope gene (env) of retroviruses. in vitro and vivo, a synthetic peptide (CKS-17) that shows homology to ISD inhibits immune function. Evidence has shown that ISD suppresses lymphocyte proliferation and allows escape from immune effectors of the innate and adaptive arms in mouse immune system. Previously, we have developed a tool ISDTool 1.0 to identify ISD of human endogenous retrovirus (HERV). However, several other important retroviruses exist and no method is devoted to ISD prediction of them so far. In the paper, a computational model is proposed to identify ISD of six typical retroviruses from three species. The model combines the minimum Redundancy Maximum Relevance (mRMR) feature selection criterion with weighted extreme learning machine (WELM) to achieve high identification accuracies of 98.95%, 96.34% and 96.87% using self-consistency, 5-fold and 10-fold cross-validation, respectively. A software tool named ISDTool 2.0 has been developed to facilitate the application of the model and a large number of new putative ISDs of the six retroviruses were predicted. In addition, motifs of ISD in these retroviruses were analyzed and the evolutionary relationship was discussed. Datasets and the software involved in the paper are available at http://sourceforge.net/projects/isdtool/files/ISDTool-2.0/.
