How to improve postgenomic knowledge discovery using imputation

  • Authors:

  • Muhammad Shoaib B. Sehgal;Iqbal Gondal;Laurence S. Dooley;Ross Coppel

  • Affiliations:

  • ARC Centre of Excellence in Bioinformatics, Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia and Victorian Bioinformatics Consortium, Monash University, VIC, ...;Gippsland School of Information Technology, Faculty of Information Technology, Monash University, Churchill, VIC, Australia;Faculty of Mathematics, Computing and Technology, The Open University, Milton Keynes, UK;Victorian Bioinformatics Consortium, Monash University, VIC, Australia and Department of Microbiology, Monash University, VIC, Australia

  • Venue:
  • EURASIP Journal on Bioinformatics and Systems Biology - Special issue on applications of signal procesing techniques to bioinformatics, genomics, and proteomics
  • Year:
  • 2009

Quantified Score

Hi-index 0.00

Visualization

Abstract

While microarrays make it feasible to rapidly investigate many complex biological problems, their multistep fabrication has the proclivity for error at every stage. The standard tactic has been to either ignore or regard erroneous gene readings as missing values, though this assumption can exert a major influence upon postgenomic knowledge discovery methods like gene selection and gene regulatory network (GRN) reconstruction. This has been the catalyst for a raft of new flexible imputation algorithms including local least square impute and the recent heuristic collateral missing value imputation, which exploit the biological transactional behaviour of functionally correlated genes to afford accurate missing value estimation. This paper examines the influence of missing value imputation techniques upon postgenomic knowledge inference methods with results for various algorithms consistently corroborating that instead of ignoring missing values, recycling microarray data by flexible and robust imputation can provide substantial performance benefits for subsequent downstream procedures