A Closed-Form Solution for Transcription Factor Activity Estimation Using Network Component Analysis
Non-iterative network component analysis (NINCA), proposed by Jacklin at.al, employs convex optimization methods to estimate the transcription factor control strengths and transcription factor activities. While NINCA provides good estimation accuracy and higher consistency, the costly optimization routine used therein renders a high computational complexity. This correspondence presents a closed form solution to estimate the connectivity matrix which is tens of times faster, and provides similar accuracy and consistency, thus making the closed form NINCA (CFNINCA) algorithm useful for large data sets encountered in practice. The proposed solution is assessed for accuracy and consistency using synthetic and yeast cell cycle data sets by comparing with the existing state-of-the-art algorithms. The robustness of the algorithm to the possible inaccuracies in prior information is also analyzed and it is observed that CFNINCA and NINCA are much more robust to erroneous prior information as compared to FastNCA.
KeywordsGene Regulatory Network transcription factor activity convex optimization
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- 2.Shmulevich, I., Saarinen, A., Yli-Harja, O., Astola, J.: Inference of genetic regulatory networks via best-fit extensions. In: Computational and Statistical Approaches to Genomics, pp. 197–210 (2003)Google Scholar
- 9.Jolliffe, I.T.: Principal component analysis, vol. 487. Springer, New York (1986)Google Scholar
- 10.Comon, P.: Independent component analysis. Higher-Order Statistics, 29–38 (1992)Google Scholar
- 12.Noor, A., Ahmad, A., Serpedin, E., Nounou, M., Nounou, H.: Robnca: Robust network component analysis for recovering transcription factor activities. Bioinformatics (2013)Google Scholar
- 17.Boyd, S., Vandenberghe, L.: Convex Optimization. Cambridge University Press (2004)Google Scholar
- 18.Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I., et al.: Transcriptional regulatory networks in saccharomyces cerevisiae. Science Signalling 298(5594), 799 (2002)Google Scholar
- 19.Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D., Futcher, B.: Comprehensive identification of cell cycle–regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 9(12), 3273–3297 (1998)CrossRefGoogle Scholar