A novel approach for prediction of multi-labeled protein subcellular localization for prokaryotic bacteria

Chia Yu Su, Allan Lo, Chin Chin Lin, Fu Chang, Wen Lian Hsu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

6 Citations (Scopus)

Abstract

We present a novel method to address multi-labeled protein subcellular localization prediction in Gram-negative bacteria using support vector machines (SVM) as classifiers. For a given protein sequence that may have more than one label, features are extracted from amino acid composition and molecular function related terms in Gene Ontology (GO) as input to SVM. We apply one-against-others SVM to proteins of Gram-negative bacteria in a 5-fold cross-validation. The results of the multi-labeled predictions are evaluated based on two criteria: class number and class category. For the first criterion, our method predicts the number of classes (class number) for each protein at an accuracy rate of 94.1%. For the second criterion, we compare the categories of the actual classes with the predicted classes proportionate to ranks, and obtain an accuracy of 83.2%. Our method is the first approach to predict and evaluate multi-labeled protein subcellular localization for prokaryotic bacteria and we demonstrate that it has a good predictive power.

Original languageEnglish
Title of host publication2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts
Pages79-80
Number of pages2
DOIs
Publication statusPublished - 2005
Externally publishedYes
Event2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts - Stanford, CA, United States
Duration: Aug 8 2005Aug 11 2005

Other

Other2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts
CountryUnited States
CityStanford, CA
Period8/8/058/11/05

Fingerprint

Bacteria
Proteins
Support vector machines
Ontology
Amino acids
Labels
Classifiers
Genes
Chemical analysis

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Su, C. Y., Lo, A., Lin, C. C., Chang, F., & Hsu, W. L. (2005). A novel approach for prediction of multi-labeled protein subcellular localization for prokaryotic bacteria. In 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts (pp. 79-80). [1540549] https://doi.org/10.1109/CSBW.2005.11

A novel approach for prediction of multi-labeled protein subcellular localization for prokaryotic bacteria. / Su, Chia Yu; Lo, Allan; Lin, Chin Chin; Chang, Fu; Hsu, Wen Lian.

2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts. 2005. p. 79-80 1540549.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Su, CY, Lo, A, Lin, CC, Chang, F & Hsu, WL 2005, A novel approach for prediction of multi-labeled protein subcellular localization for prokaryotic bacteria. in 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts., 1540549, pp. 79-80, 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts, Stanford, CA, United States, 8/8/05. https://doi.org/10.1109/CSBW.2005.11
Su CY, Lo A, Lin CC, Chang F, Hsu WL. A novel approach for prediction of multi-labeled protein subcellular localization for prokaryotic bacteria. In 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts. 2005. p. 79-80. 1540549 https://doi.org/10.1109/CSBW.2005.11
Su, Chia Yu ; Lo, Allan ; Lin, Chin Chin ; Chang, Fu ; Hsu, Wen Lian. / A novel approach for prediction of multi-labeled protein subcellular localization for prokaryotic bacteria. 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts. 2005. pp. 79-80
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