Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways

BMC Bioinformatics

Volumn 11, Issue SUPPLL.1, 2010, Pages

  Mano, Adi ^a,c   Tuller, Tamir ^b,d   Béjà, Oded ^a   Pinter, Ron Y ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^b TEL AVIV UNIVERSITY   (Israel)

^c Google Inc   (Israel)

^d WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL OBSERVATIONS; CELLULAR CIRCUITRY; COMPARATIVE ANALYSIS; COMPUTATIONAL APPROACH; GENOMIC SEQUENCE; METABOLIC NETWORK; METABOLIC PATHWAYS; UNIFIED FRAMEWORK;

GENES; PIPELINES; BIOINFORMATICS;

METABOLISM;

ARCHAEA;

PROTEIN;

ARCHAEBACTERIUM; ARTICLE; COMPARATIVE STUDY; GENETICS; GENOME; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY; SPECIES DIFFERENCE;

ARCHAEA; EVOLUTION, MOLECULAR; GENOME; METABOLIC NETWORKS AND PATHWAYS; PHYLOGENY; PROTEINS; SPECIES SPECIFICITY;

EID: 75149156665     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S1-S38     Document Type: Article

References (32)

1. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, (34 Database):D354-357. 10.1093/nar/gkj102, 1347464, 16381885.
2. Caspi R, Foerster H, Fulcher CA, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee SY, et al. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 2006, (34 Database):D511-516. 10.1093/nar/gkj128, 1347490, 16381923.
3. Letunic I, Yamada T, Kanehisa M, Bork P. iPath: interactive exploration of biochemical pathways and networks. Trends Biochem Sci 2008, 33(3):101-103. Epub 2008 Feb 2013., 10.1016/j.tibs.2008.01.001, 18276143.
4. BioCarta. , http://www.biocarta.com
5. Pinter RY, Rokhlenko O, Yeger-Lotem E, Ziv-Ukelson M. Alignment of metabolic pathways. Bioinformatics 2005, 21(16):3401-3408. 10.1093/bioinformatics/bti554, 15985496.
6. Tohsato Y, Matsuda H, Hashimoto A. A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy. Proc Int Conf Intell Syst Mol Biol 2000, 8:376-383.
7. Sharan R, Ideker T. Modeling cellular machinery through biological network comparison. Nat Biotechnol 2006, 24(4):427-433. 10.1038/nbt1196, 16601728.
8. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2007, (35 Database):D5-12. 10.1093/nar/gkl1031, 1781113, 17170002.
9. Dandekar T, Schuster S, Snel B, Huynen M, Bork P. Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem J 1999, 343(Pt 1):115-124. 10.1042/0264-6021:3430115, 1220531, 10493919.
10. Clemente JC, Satou K, Valiente G. Finding conserved and non-conserved reactions using a metabolic pathway alignment algorithm. Genome Inform 2006, 17(2):46-56.
11. Forst CV, Schulten K. Evolution of metabolisms: a new method for the comparison of metabolic pathways using genomics information. J Comput Biol 1999, 6(3-4):343-360. 10.1089/106652799318319, 10582571.
12. Forst CV, Schulten K. Phylogenetic analysis of metabolic pathways. J Mol Evol 2001, 52(6):471-489.
13. Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci USA 2002, 99(19):12246-12251. 10.1073/pnas.182432999, 129430, 12218172.
14. Heymans M, Singh AK. Deriving phylogenetic trees from the similarity analysis of metabolic pathways. Bioinformatics 2003, 19(Suppl 1):i138-146. 10.1093/bioinformatics/btg1018, 12855450.
15. Clemente JC, Satou K, Valiente G. Reconstruction of phylogenetic relationships from metabolic pathways based on the enzyme hierarchy and the gene ontology. Genome Inform 2005, 16(2):45-55.
16. Clemente JC, Satou K, Valiente G. Phylogenetic reconstruction from non-genomic data. Bioinformatics 2007, 23(2):e110-115. 10.1093/bioinformatics/btl307, 17237077.
17. Hong SH, Kim TY, Lee SY. Phylogenetic analysis based on genome-scale metabolic pathway reaction content. Appl Microbiol Biotechnol 2004, 65(2):203-210. Epub 2004 Jun 2009., 10.1007/s00253-004-1641-3, 15197509.
18. Chor B, Tuller T. Biological networks: comparison, conservation, and evolution via relative description length. J Comput Biol 2007, 14(6):817-838. 10.1089/cmb.2007.R018, 17691896.
19. Tuller T, Kupiec M, Ruppin E. Co-evolutionary networks of genes and cellular processes across fungal species. Genome Biol 2009, 10(5):R48. 10.1186/gb-2009-10-5-r48, 2718514, 19416514.
20. Chen Y, Dokholyan NV. The coordinated evolution of yeast proteins is constrained by functional modularity. Trends Genet 2006, 22(8):416-419. 10.1016/j.tig.2006.06.008, 16797778.
21. Juan D, Pazos F, Valencia A. High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc Natl Acad Sci USA 2008, 105(3):934-939. 10.1073/pnas.0709671105, 2242690, 18199838.
22. Spirin V, Gelfand MS, Mironov AA, Mirny LA. A metabolic network in the evolutionary context: multiscale structure and modularity. Proc Natl Acad Sci USA 2006, 103(23):8774-8779. 10.1073/pnas.0510258103, 1482654, 16731630.
23. Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, et al. STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 2009, (37 Database):D412-416. 10.1093/nar/gkn760, 2686466, 18940858.
24. Shannon CE. A mathematical theory of communication. Bell System Technical Journal 1948, 29:379-423. and 623-656.
25. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4(4):406-425.
26. Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 1989, 5:164-166.
27. Madigan M, Martinko J, Parker J. Brock Biology of Microorganisms. 2003, Pearson Education, Inc, 10.
28. Dai YRRD, Millstein JH, Hartzell PL, Grahame DA, DeMoll E. Acetyl-CoA decarbonylase/synthase complex from Archaeoglobus fulgidus. Arch Microbiol 1998, 169:525-529. 10.1007/s002030050606, 9575239.
29. Daugherty M, Vonstein V, Overbeek R, Osterman A. Archaeal shikimate kinase, a new member of the GHMP-kinase family. J Bacteriol 2001, 183(1):292-300. 10.1128/JB.183.1.292-300.2001, 94878, 11114929.
30. Orita I, Sato T, Yurimoto H, Kato N, Atomi H, Imanaka T, Sakai Y. The ribulose monophosphate pathway substitutes for the missing pentose phosphate pathway in the archaeon Thermococcus kodakaraensis. J Bacteriol 2006, 188(13):4698-4704. 10.1128/JB.00492-06, 1482999, 16788179.
31. Spanheimer R, Muller V. The molecular basis of salt adaptation in Methanosarcina mazei Go1. Arch Microbiol 2008, 190(3):271-279. 10.1007/s00203-008-0363-9, 18379758.
32. Sharan R, Shamir R. CLICK: a clustering algorithm with applications to gene expression analysis. Proc Int Conf Intell Syst Mol Biol 2000, 8:307-316.