Identification of Shared Components and Sparse Networks in Gene Expression Time-Course Data

High-throughput gene expression technologies such as microarrays have been utilized in a variety of scientific applications. In this article, we develop multivariate techniques for visualizing gene regulatory networks using independent components analysis (ICA) techniques. A desirable feature of the ICA method is that it approximates a biological model for the gene expression. The methods are outlined and illustrated with application to yeast gene expression data.

[1]  Wolfram Liebermeister,et al.  Linear modes of gene expression determined by independent component analysis , 2002, Bioinform..

[2]  Hiroaki Kitano,et al.  Foundations of systems biology , 2001 .

[3]  D. Thieffry,et al.  The modularity of biological regulatory networks. , 1999, Bio Systems.

[4]  Joshua M. Stuart,et al.  MICROARRAY EXPERIMENTS : APPLICATION TO SPORULATION TIME SERIES , 1999 .

[5]  W. Wong,et al.  Transitive functional annotation by shortest-path analysis of gene expression data , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Kevin Atteson,et al.  Constraint structure analysis of gene expression , 2000, Functional & Integrative Genomics.

[7]  Yaniv Ziv,et al.  Revealing modular organization in the yeast transcriptional network , 2002, Nature Genetics.

[8]  Michael E. Tipping,et al.  Probabilistic Principal Component Analysis , 1999 .

[9]  John W. Tukey,et al.  A Projection Pursuit Algorithm for Exploratory Data Analysis , 1974, IEEE Transactions on Computers.

[10]  Erkki Oja,et al.  Independent Component Analysis , 2001 .

[11]  A. Barabasi,et al.  Lethality and centrality in protein networks , 2001, Nature.

[12]  S. Dudoit,et al.  STATISTICAL METHODS FOR IDENTIFYING DIFFERENTIALLY EXPRESSED GENES IN REPLICATED cDNA MICROARRAY EXPERIMENTS , 2002 .

[13]  Aapo Hyvärinen,et al.  Fast and robust fixed-point algorithms for independent component analysis , 1999, IEEE Trans. Neural Networks.

[14]  R. Albert,et al.  The large-scale organization of metabolic networks , 2000, Nature.

[15]  D. Botstein,et al.  Singular value decomposition for genome-wide expression data processing and modeling. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Michael Ruogu Zhang,et al.  Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. , 1998, Molecular biology of the cell.

[17]  D. Pe’er,et al.  Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data , 2003, Nature Genetics.

[18]  Tommi S. Jaakkola,et al.  Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks , 2000, Pacific Symposium on Biocomputing.

[19]  Neal S. Holter,et al.  Dynamic modeling of gene expression data. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[20]  H. Bussemaker,et al.  Regulatory element detection using correlation with expression , 2001, Nature Genetics.

[21]  J. Blake,et al.  Creating the Gene Ontology Resource : Design and Implementation The Gene Ontology Consortium 2 , 2001 .

[22]  Jesper Tegnér,et al.  Reverse engineering gene networks using singular value decomposition and robust regression , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[23]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[24]  Patrik D'haeseleer,et al.  Linear Modeling of mRNA Expression Levels During CNS Development and Injury , 1998, Pacific Symposium on Biocomputing.

[25]  J. Friedman Exploratory Projection Pursuit , 1987 .

[26]  B. Silverman,et al.  Functional Data Analysis , 1997 .

[27]  Gary A. Churchill,et al.  Analysis of Variance for Gene Expression Microarray Data , 2000, J. Comput. Biol..

[28]  T. Ideker,et al.  A new approach to decoding life: systems biology. , 2001, Annual review of genomics and human genetics.