Predicting genes for orphan metabolic activities using phylogenetic profiles 英文参考文献.docVIP

Open Access Method 2006ChenVolumande 7,VitkupIssue 2, Article R17 Predicting genes for orphan metabolic activities using phylogenetic profiles Lifeng Chen and Dennis Vitkup Address: Center for Computational Biology and Bioinformatics and Department of Biomedical Informatics, Columbia University, St Nicholas Avenue, Irving Cancer Research Center, New York, NY 10032, USA. Correspondence: Dennis Vitkup. Email: vitkup@ Published: 15 February 2006 Received: 1 September 2005 Revised: 1 December 2005 Accepted: 12 January 2006 Genome Biology 2006, 7:R17 (doi:10.1186/gb-2006-7-2-r17) The electronic version of this article is the complete one and can be found online at /2006/7/2/R17 ? 2006 Chen and Vitkup; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. OrphanorpphAanmmmetabolicetehtoadbotlhicataactivitiescombinesctivities inlocalyeasstructuret and itofEsachmetabolicerichia conetworkli/it.with/p phylogenetic profiles is described and used to assign genes to Abstract Homology-based methods fail to assign genes to many metabolic activities present in sequenced organisms. To suggest genes for these orphan activities we developed a novel method that efficiently combines local structure of a metabolic network with phylogenetic profiles. We validated our method using known metabolic genes in Saccharomyces cerevisiae and Escherichia coli. We show that our method should be easily transferable to other organisms, and that it is robust to errors in incomplete metabolic networks. Background The inability to annotate all enzymes using homology-based methods leaves members of metabolic pathways missing [12]. That is, although biochemical evidence may indicate that a certain group of reactions takes place in an organis