Specificity of transporter associated with antigen processing protein as revealed by feature selection method

Xue Ling Li, Shu Lin Wang, Mei Ling Hou

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Peptide fragments that serve as the cytotoxic T lymphocyte (CTL) epitopes are processed from antigens by the proteasome and then are transported to the endoplasmic reticulum through transporter associated with antigen processing (TAP) before being loaded onto the MHC class I molecule. Here, we studied TAP specificity by a neighborhood rough set (NRS) model based feature selection and prioritization method. By means of binary, amino acid properties, and binary plus properties of amino acids encoding, respectively, we adopted NRS based feature selection method to select multiple optimal feature sets for TAP binding peptides binary classification. The features in these optimal sets were ranked according to their occurrence frequency. Results show that the NRS is effective for prediction improvement and analysis of the specificity of TAP transporter. The proposed method can be used as a tool for predicting TAP binding peptides and be useful for subunit vaccine rational design and related bioinformatics cases.

Original languageEnglish (US)
Pages (from-to)1129-1135
Number of pages7
JournalProtein and Peptide Letters
Volume17
Issue number9
DOIs
StatePublished - Sep 2010
Externally publishedYes

Fingerprint

trypsinogen activation peptide
Antigen Presentation
Feature extraction
Antigens
Amino Acids
Peptides
Subunit Vaccines
Peptide Fragments
T-Lymphocyte Epitopes
Proteasome Endopeptidase Complex
Bioinformatics
Processing
Proteins
Cytotoxic T-Lymphocytes
Computational Biology
Endoplasmic Reticulum
Molecules
transporter associated with antigen processing (TAP)

Keywords

  • Feature prioritization
  • Neighborhood rough set
  • Peptide
  • Specificity
  • SVM
  • TAP

ASJC Scopus subject areas

  • Biochemistry
  • Structural Biology

Cite this

Specificity of transporter associated with antigen processing protein as revealed by feature selection method. / Li, Xue Ling; Wang, Shu Lin; Hou, Mei Ling.

In: Protein and Peptide Letters, Vol. 17, No. 9, 09.2010, p. 1129-1135.

Research output: Contribution to journalArticle

Li, Xue Ling ; Wang, Shu Lin ; Hou, Mei Ling. / Specificity of transporter associated with antigen processing protein as revealed by feature selection method. In: Protein and Peptide Letters. 2010 ; Vol. 17, No. 9. pp. 1129-1135.
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