Abstract
Background: 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. Methods: 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. Result: 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.
Highlights
The endoplasmic reticulum (ER) is an important subcellular organelle in eukaryotic cells
In order to explain our method properly, we developed a new set of matrix-based notations to describe the Type-II classic pseudo-amino acid compositions, known as the amphiphilic pseudo-amino acid compositions (Chou, 2005)
Our method achieved a sensitivity of 83.06% and a specificity of 86.38%, which are both higher than the values for ERPred on the same dataset
Summary
The endoplasmic reticulum (ER) is an important subcellular organelle in eukaryotic cells. Two major functions are usually recognized for ER One is that it selectively transports secreted proteins and membrane proteins. The ER proteins are sorted precisely with quality controls (Ellgaard and Helenius, 2003; Araki and Nagata, 2011). An understanding of these processes contributes to the elucidation of endoplasmic reticulum function and the pathogenesis of many diseases (Paschen and Frandsen, 2001; Verkhratsky, 2002). 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 difference between the ER-resident proteins and other nonresident proteins should be carefully studied
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