Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data

• DOI: 10.1093/bioinformatics/btn131
• Publication Date: 2008-04-10T00:25:09Z
• Authors: Chunqi Chang; Zhi Ding; Yeung Sam Hung; Peter Chin Wan Fung
• Keywords: Component (thermodynamics); Gene regulatory network

Abstract Motivation: Recently developed network component analysis (NCA) approach is promising for gene regulatory reconstruction from microarray data. The existing NCA algorithm an iterative method which has two potential limitations: computational instability and multiple local solutions. subsequently NCA-r with Tikhonov regularization can help solve the first issue but cannot completely handle second one. Here we develop a novel Fast Network Component Analysis (FastNCA) analytical solution that much faster does not have above limitations. Results: Firstly FastNCA compared to using synthetic of more accurate than comparable properly converged NCA. sensitive correlation among input signals, while its performance degrade little as dramatically Like NCA, very small inaccuracies in priori information on topology. about several tens times hundreds NCA-r. Then, applied real yeast cell-cycle activities estimated regulators by are semi-quantitative results obtained independently Lee et al. (2002). It shown here there greater agreement between Lee's, represented ratio 23/33, 14/33. Availability: Software supplementary materials available http://www.eee.hku.hk/~cqchang/FastNCA.htm Contact: [e-mail]