Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria

Fruzangohar, Mario and Ebrahimie, Esmaeil and Ogunniyi, Abiodun D. and Mahdi, Layla K. and Paton, James C. and Adelson, David L. (2013) Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria. PLoS One, 8 (3). e58759-e58767.

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Abstract

The primary means of classifying new functions for genes and proteins relies on Gene Ontology (GO), which defines genes/proteins using a controlled vocabulary in terms of their Molecular Function, Biological Process and Cellular Component. The challenge is to present this information to researchers to compare and discover patterns in multiple datasets using visually comprehensible and user-friendly statistical reports. Importantly, while there are many GO resources available for eukaryotes, there are none suitable for simultaneous, graphical and statistical comparison between multiple datasets. In addition, none of them supports comprehensive resources for bacteria. By using Streptococcus pneumoniae as a model, we identified and collected GO resources including genes, proteins, taxonomy and GO relationships from NCBI, UniProt and GO organisations. Then, we designed database tables in PostgreSQL database server and developed a Java application to extract data from source files and loaded into database automatically. We developed a PHP web application based on Model-View-Control architecture, used a specific data structure as well as current and novel algorithms to estimate GO graphs parameters. We designed different navigation and visualization methods on the graphs and integrated these into graphical reports. This tool is particularly significant when comparing GO groups between multiple samples (including those of pathogenic bacteria) from different sources simultaneously. Comparing GO protein distribution among up- or downregulated genes from different samples can improve understanding of biological pathways, and mechanism(s) of infection. It can also aid in the discovery of genes associated with specific function(s) for investigation as a novel vaccine or therapeutic targets.


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Item Type: Article (Commonwealth Reporting Category C)
Refereed: Yes
Item Status: Live Archive
Additional Information: Published version made available in accordance with Creative Commons Attribution License 4.0.
Faculty / Department / School: Historic - Faculty of Sciences - No Department
Date Deposited: 03 Aug 2016 03:39
Last Modified: 27 Mar 2017 05:27
Fields of Research : 06 Biological Sciences > 0605 Microbiology > 060503 Microbial Genetics
08 Information and Computing Sciences > 0803 Computer Software > 080301 Bioinformatics Software
Socio-Economic Objective: E Expanding Knowledge > 97 Expanding Knowledge > 970106 Expanding Knowledge in the Biological Sciences
E Expanding Knowledge > 97 Expanding Knowledge > 970108 Expanding Knowledge in the Information and Computing Sciences
Funding Details:
Identification Number or DOI: 10.1371/journal.pone.0058759
URI: http://eprints.usq.edu.au/id/eprint/28817

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