Journal of Proteomics & Bioinformatics
Open Access

Ahmad Barghash

Publications

• Research Article
  Annotating the Function of Protein-coding Genes Based on Gene Ontology Terms of Neighboring Co-expressed Genes
  Author(s): Vu Ha Tran, Ahmad Barghash and Volkhard HelmsVu Ha Tran, Ahmad Barghash and Volkhard Helms
  
  Proteins are of key importance in virtually every cellular process but many proteins have still not been annotated with functions due to experimental difficulties involved with functional assays. To address this problem, many computational methods based on sequence homology, three-dimensional structure, genomic context, and gene expression were developed to predict functions of proteins. Here, we tested the performance of a novel approach that is motivated by the concept of bacterial operons. To predict the substrate specificities of membrane transporters we combined genomic context-based methods with Gene Ontology and gene expression data whereby using SVM for classifying genes. We found that in Escherichia coli, the substrate-specificities of membrane transporters can be predicted with ca. 90% accuracy from the biological functions of co-expressed neighboring genes. In Saccharomyces.. View More»
  DOI: 10.4172/jpb.1000468

  Abstract PDF

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