A PATHWAY APPROACH TO ALIGN REGULATORY-METABOLIC NETWORKS

Y. LI1,2,3,∗, J.J. BOT, M.J.T. REINDERS and D. DE RIDDER Information & Communication Theory Group, Faculty of Electrical Eng., Mathematics & Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands 2 Netherlands Bioinformatics Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands 3 Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands ∗Email: y.li@tudelft.nl

[1]  Marcel J. T. Reinders,et al.  Metabolic pathway alignment between species using a comprehensive and flexible similarity measure , 2008, BMC Systems Biology.

[2]  Julio Collado-Vides,et al.  RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation , 2007, Nucleic Acids Res..

[3]  Marcel J. T. Reinders,et al.  Metabolic Pathway Alignment (M-Pal) Reveals Diversity and Alternatives in Conserved Networks , 2007, APBC.

[4]  Erik van Nimwegen,et al.  SwissRegulon: a database of genome-wide annotations of regulatory sites , 2006, Nucleic Acids Res..

[5]  T. Ideker,et al.  Modeling cellular machinery through biological network comparison , 2006, Nature Biotechnology.

[6]  Pooja Jain,et al.  The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae , 2005, Nucleic Acids Res..

[7]  Szymon M. Kielbasa,et al.  Measuring similarities between transcription factor binding sites , 2005, BMC Bioinformatics.

[8]  A. Regev,et al.  Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[9]  J. Nielsen,et al.  Uncovering transcriptional regulation of metabolism by using metabolic network topology. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Michael Q. Zhang,et al.  Similarity of position frequency matrices for transcription factor binding sites , 2005, Bioinform..

[11]  Michael Q. Zhang,et al.  Identifying tissue-selective transcription factor binding sites in vertebrate promoters. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Peter D. Karp,et al.  EcoCyc: a comprehensive database resource for Escherichia coli , 2004, Nucleic Acids Res..

[13]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt) , 2004, Nucleic Acids Res..

[14]  Alan M. Moses,et al.  Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi , 2004, PLoS biology.

[15]  W. Wasserman,et al.  Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus. , 2004, Genome research.

[16]  Markus J. Herrgård,et al.  Integrating high-throughput and computational data elucidates bacterial networks , 2004, Nature.

[17]  A. Sandelin,et al.  Applied bioinformatics for the identification of regulatory elements , 2004, Nature Reviews Genetics.

[18]  Ambuj K. Singh,et al.  Deriving phylogenetic trees from the similarity analysis of metabolic pathways , 2003, ISMB.

[19]  S. Teichmann,et al.  Evolution of transcription factors and the gene regulatory network in Escherichia coli. , 2003, Nucleic acids research.

[20]  An-Ping Zeng,et al.  Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms , 2003, Bioinform..

[21]  A. Barabasi,et al.  Hierarchical Organization of Modularity in Metabolic Networks , 2002, Science.

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

[23]  M. Huynen,et al.  Neutral evolution of mutational robustness. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Gary D. Stormo,et al.  MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices , 1995, Comput. Appl. Biosci..

[25]  A. Murzin Can homologous proteins evolve different enzymatic activities? , 1993, Trends in biochemical sciences.

[26]  L. Hedges,et al.  Statistical Methods for Meta-Analysis , 1987 .

[27]  Marcel J. T. Reinders,et al.  Integration of prior knowledge of measurement noise in kernel density classification , 2008, Pattern Recognit..

[28]  Jan Ihmels,et al.  Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae , 2004, Nature Biotechnology.

[29]  Robert D. Finn,et al.  The Pfam protein families database , 2004, Nucleic Acids Res..

[30]  Xin Chen,et al.  The TRANSFAC system on gene expression regulation , 2001, Nucleic Acids Res..

[31]  David Ghosh,et al.  OOTFD (Object-Oriented Transcription Factors Database): an object- oriented successor to TFD , 1998, Nucleic Acids Res..

[32]  Susumu Goto,et al.  LIGAND: chemical database for enzyme reactions , 1998, Bioinform..