Augmented transitive relationships with high impact protein distillation in protein interaction prediction

Yi Tsung Tang, Hung-Yu Kao

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Predicting new protein-protein interactions is important for discovering novel functions of various biological pathways. Predicting these interactions is a crucial and challenging task. Moreover, discovering new protein-protein interactions through biological experiments is still difficult. Therefore, it is increasingly important to discover new protein interactions. Many studies have predicted protein-protein interactions, using biological features such as Gene Ontology (GO) functional annotations and structural domains of two proteins. In this paper, we propose an augmented transitive relationships predictor (ATRP), a new method of predicting potential protein interactions using transitive relationships and annotations of protein interactions. In addition, a distillation of virtual direct protein-protein interactions is proposed to deal with unbalanced distribution of different types of interactions in the existing protein-protein interaction databases. Our results demonstrate that ATRP can effectively predict protein-protein interactions. ATRP achieves an 81% precision, a 74% recall and a 77% F-measure in average rate in the prediction of direct protein-protein interactions. Using the generated benchmark datasets from KUPS to evaluate of all types of the protein-protein interaction, ATRP achieved a 93% precision, a 49% recall and a 64% F-measure in average rate. This article is part of a Special Issue entitled: Computational Methods for Protein Interaction and Structural Prediction.

Original languageEnglish
Pages (from-to)1468-1475
Number of pages8
JournalBiochimica et Biophysica Acta - Proteins and Proteomics
Volume1824
Issue number12
DOIs
Publication statusPublished - 2012 Dec 1

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Distillation
Proteins
Molecular Sequence Annotation
Benchmarking
Protein Databases
Gene Ontology

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Biophysics
  • Analytical Chemistry
  • Molecular Biology

Cite this

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Augmented transitive relationships with high impact protein distillation in protein interaction prediction. / Tang, Yi Tsung; Kao, Hung-Yu.

In: Biochimica et Biophysica Acta - Proteins and Proteomics, Vol. 1824, No. 12, 01.12.2012, p. 1468-1475.

Research output: Contribution to journalArticle

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