Reconstruction of genetic association networks from microarray data: a partial least squares approach

Bioinformatics
Vasyl PihurSusmita Datta

Abstract

Gene association/interaction networks provide vast amounts of information about essential processes inside the cell. A complete picture of gene-gene associations/interactions would open new horizons for biologists, ranging from pure appreciation to successful manipulation of biological pathways for therapeutic purposes. Therefore, identification of important biological complexes whose members (genes and their products proteins) interact with each other is of prime importance. Numerous experimental methods exist but, for the most part, they are costly and labor intensive. Computational techniques, such as the one proposed in this work, provide a quick 'budget' solution that can be used as a screening tool before more expensive techniques are attempted. Here, we introduce a novel computational method based on the partial least squares (PLS) regression technique for reconstruction of genetic networks from microarray data. The proposed PLS method is shown to be an effective screening procedure for the detection of gene-gene interactions from microarray data. Both simulated and real microarray experiments show that the PLS-based approach is superior to its competitors both in terms of performance and applicability. R code is availab...Continue Reading

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Citations

Nov 26, 2009·BMC Bioinformatics·Nicole KrämerAnne-Laure Boulesteix
Feb 2, 2010·BMC Bioinformatics·Ritesh KrishnaVicky Buchanan-Wollaston
Feb 23, 2010·BMC Bioinformatics·Ryan GillSusmita Datta
May 21, 2011·BMC Medical Genomics·Xiaohong LiSusmita Datta
Sep 3, 2010·Journal of Perinatal Medicine·Berit DahlstrømGeir Bukholm
Nov 22, 2014·Chemometrics and Intelligent Laboratory Systems : an International Journal Sponsored by the Chemometrics Society·Imhoi KooXiang Zhang
Feb 13, 2016·Scientific Reports·Nooshin OmranianZoran Nikoloski
Jul 27, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yinyin YuanFlorian Markowetz
May 1, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Arthur TenenhausVincent Frouin
Aug 26, 2014·Journal of Bioinformatics and Computational Biology·Imhoi KooSeongho Kim
Mar 31, 2015·PloS One·Maiju KujalaSusmita Datta
Dec 1, 2017·Bioinformatics·Phan Nguyen, Rosemary Braun
Apr 28, 2018·Scientific Reports·Shayan Tabe-BordbarSaurabh Sinha
May 24, 2018·Biology Direct·Alejandro R WalkerSusmita Datta
Nov 8, 2018·International Journal of Genomics·Jiajia Chen, Liangzhi Li

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