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

Bioinformatics
Chunqi ChangPeter Chin Wan Fung

Abstract

Recently developed network component analysis (NCA) approach is promising for gene regulatory network reconstruction from microarray data. The existing NCA algorithm is an iterative method which has two potential limitations: computational instability and multiple local solutions. The subsequently developed NCA-r algorithm with Tikhonov regularization can help solve the first issue but cannot completely handle the second one. Here we develop a novel Fast Network Component Analysis (FastNCA) algorithm which has an analytical solution that is much faster and does not have the above limitations. Firstly FastNCA is compared to NCA and NCA-r using synthetic data. The reconstruction of FastNCA is more accurate than that of NCA-r and comparable to that of properly converged NCA. FastNCA is not sensitive to the correlation among the input signals, while its performance does degrade a little but not as dramatically as that of NCA. Like NCA, FastNCA is not very sensitive to small inaccuracies in a priori information on the network topology. FastNCA is about several tens times faster than NCA and several hundreds times faster than NCA-r. Then, the method is applied to real yeast cell-cycle microarray data. The activities of the estimated ...Continue Reading

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