AUTHOR=Miao Yang-Yang , Zhao Wei , Li Guang-Ping , Gao Yang , Du Pu-Feng 

TITLE=Predicting Endoplasmic Reticulum Resident Proteins Using Auto-Cross Covariance Transformation With a U-Shaped Residue Weight-Transfer Function

JOURNAL=Frontiers in Genetics

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2019.01231

DOI=10.3389/fgene.2019.01231

ISSN=1664-8021

ABSTRACT=<p><bold>Background:</bold> The endoplasmic reticulum (ER) is an important organelle in eukaryotic cells. It is involved in many important biological processes, such as cell metabolism, protein synthesis, and post-translational modification. The proteins that reside within the ER are called ER-resident proteins. These proteins are closely related to the biological functions of the ER. The difference between the ER-resident proteins and other non-resident proteins should be carefully studied.</p><p><bold>Methods:</bold> We developed a support vector machine (SVM)-based method. We developed a U-shaped weight-transfer function and used it, along with the positional-specific physiochemical properties (PSPCP), to integrate together sequence order information, signaling peptides information, and evolutionary information.</p><p><bold>Result:</bold> Our method achieved over 86% accuracy in a jackknife test. We also achieved roughly 86% sensitivity and 67% specificity in an independent dataset test. Our method is capable of identifying ER-resident proteins.</p>