Predicting phenotypic traits of prokaryotes from protein domain frequencies

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Lingner, Thomas ^a,b   Mühlhausen, Stefanie ^a   Gabaldón, Toni ^b   Notredame, Cedric ^b   Meinicke, Peter ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

^b CENTRE FOR GENOMIC REGULATION CRG   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURATE PREDICTION; ANNOTATION ERRORS; BIOLOGICAL INSIGHT; EXPERIMENTAL CHARACTERIZATION; GENOME SEQUENCES; MACHINE LEARNING APPROACHES; PHENOTYPIC TRAITS; PREDICTION ACCURACY;

GENES; GENETIC ENGINEERING; MICROORGANISMS; PROTEINS; SYSTEMATIC ERRORS;

FORECASTING;

PROKARYOTA;

BACTERIAL PROTEIN;

ALGORITHM; ARCHAEAL GENOME; ARTICLE; BACTERIAL GENOME; CHEMISTRY; MOLECULAR GENETICS; PHENOTYPE; PROTEIN TERTIARY STRUCTURE;

ALGORITHMS; BACTERIAL PROTEINS; GENOME, ARCHAEAL; GENOME, BACTERIAL; MOLECULAR SEQUENCE ANNOTATION; PHENOTYPE; PROTEIN STRUCTURE, TERTIARY;

EID: 77956897429     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-481     Document Type: Article

References (30)

1. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA 1999, 96:4285-4288. 10.1073/pnas.96.8.4285, 16324, 10200254.
2. Kensche PR, van Noort V, Dutilh BE, Huynen MA. Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. J R Soc Interface 2008, 5:151-170. 10.1098/rsif.2007.1047, 2405902, 17535793.
3. Gabaldón T, Dessimoz C, Huxley-Jones J, Vilella AJ, Sonnhammer EL, Lewis S. Joining forces in the quest for orthologs. Genome Biol 2009, 10:403. 10.1186/gb-2009-10-9-403, 2768974, 19785718.
4. Jim K, Parmar K, Singh M, Tavazoie S. A cross-genomic approach for systematic mapping of phenotypic traits to genes. Genome Res 2004, 14:109-115. 10.1101/gr.1586704, 314287, 14707173.
5. Liu Y, Li J, Sam L, Goh CS, Gerstein M, Lussier YA. An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits. PLoS Comput Biol 2006, 2:e159. 10.1371/journal.pcbi.0020159, 1636675,1636675, 17112314.
6. Slonim N, Elemento O, Tavazoie S. Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks. Mol Syst Biol 2006, 2:2006.0005. 10.1038/msb4100047, 1681479, 16732191.
7. Tamura M, D'haeseleer P. Microbial genotype-phenotype mapping by class association rule mining. Bioinformatics 2008, 24:1523-1529. 10.1093/bioinformatics/btn210, 2718668, 18467347.
8. Kastenmüller G, Schenk ME, Gasteiger J, Mewes HW. Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes. Genome Biol 2009, 10:R28. 10.1186/gb-2009-10-3-r28, 2690999, 19284550.
9. Lasken RS. Single-cell genomic sequencing using Multiple Displacement Amplification. Curr Opin Microbiol 2007, 10:510-516. 10.1016/j.mib.2007.08.005, 17923430.
10. Ishoey T, Woyke T, Stepanauskas R, Novotny M, Lasken RS. Genomic sequencing of single microbial cells from environmental samples. Curr Opin Microbiol 2008, 11:198-204. 10.1016/j.mib.2008.05.006, 18550420.
11. Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P. A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev 2008, 72:557-578. 10.1128/MMBR.00009-08, 2593568, 19052320.
12. Woyke T, Xie G, Copeland A, Gonzalez JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R. Assembling the marine metagenome, one cell at a time. PLoS ONE 2009, 4:e5299. 10.1371/journal.pone.0005299, 2668756, 19390573.
13. Sammut S, Finn R, Bateman A. Pfam 10 years on: 10,000 families and still growing. Brief Bioinformatics 2008, 9:210-219. 10.1093/bib/bbn010, 18344544.
14. Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res 2002, 30:281-283. 10.1093/nar/30.1.281, 99109, 11752315.
15. Meinicke P. UFO: a web server for ultra-fast functional profiling of whole genome protein sequences. BMC Genomics 2009, 10:409. 10.1186/1471-2164-10-409, 2744726, 19725959.
16. Davis J, Goadrich M. The relationship between Precision-Recall and ROC curves. ICML '06: Proceedings of the 23rd international conference on Machine learning 2006, 233-240. New York, NY, USA: ACM.
17. Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997, 278:631-637. 10.1126/science.278.5338.631, 9381173.
18. Takamatsu H, Imamura A, Kodama T, Asai K, Ogasawara N, Watabe K. The yabG gene of Bacillus subtilis encodes a sporulation specific protease which is involved in the processing of several spore coat proteins. FEMS Microbiol Lett 2000, 192:33-38. 10.1111/j.1574-6968.2000.tb09355.x, 11040425.
19. Zhao K, Liu M, Burgess RR. Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis. Nucleic Acids Res 2009,
20. Kim J, Kang Y, Choi O, Jeong Y, Jeong JE, Lim JY, Kim M, Moon JS, Suga H, Hwang I. Regulation of polar flagellum genes is mediated by quorum sensing and FlhDC in Burkholderia glumae. Mol Microbiol 2007, 64:165-179. 10.1111/j.1365-2958.2007.05646.x, 17376080.
21. Homaster AR, Hill KK, Gee JE, Marston CK, De BK, Popovic T, Sue D, Wilkins PP, Avashia SB, Drumgoole R, Helma CH, Ticknor LO, Okinaka RT, Jackson PJ. Characterization of Bacillus cereus isolates associated with fatal pneumonias: strains are closely related to Bacillus anthracis and harbor B. anthracis virulence genes. J Clin Microbiol 2006, 44:3352-3360. 10.1128/JCM.00561-06, 1594744, 16954272.
22. Holdeman LV, Moore WEC. New Genus, Coprococcus, Twelve New Species, and Emended Descriptions of Four Previously Described Species of Bacteria from Human Feces. Int J Syst Bacteriol 1974, 24(2):260-277.
23. Mevs U, Stackebrandt E, Schumann P, Gallikowski C, Hirsch P. Modestobacter multiseptatus gen. nov., sp. nov., a budding actinomycete from soils of the Asgard Range (Transantarctic Mountains). Int J Syst Evol Microbiol 2000, 50:337-346.
24. Magot M, Ravot G, Campaignolle X, Ollivier B, Patel BKC, Fardeau ML, Thomas P, Crolet JL, Garcia JL. Dethiosulfovibrio peptidovorans gen. nov., sp. nov., a New Anaerobic, Slightly Halophilic, Thiosulfate-Reducing Bacterium from Corroding Offshore Oil Wells. Int J Syst Bacteriol 1997, 47(3):818-824. 10.1099/00207713-47-3-818, 9226912.
25. Clum A, Nolan M, Lang E, Rio TGD, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Göker M, Spring S, Land M, Hauser L, Chang YJ, Jeffries C, Chain P, Bristow J, Eisen J, Markowitz V, Hugenholtz P, Kyrpides N, Klenk HP, Lapidus A. Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT). Standards in Genomic Sciences 2009, 1.
26. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
27. Rifkin R, Yeo G, Poggio T. Regularized Least Squares Classification. Advances in Learning Theory: Methods, Model and Applications NATO Science Series III: Computer and Systems Sciences 2003, 190:131-153. Amsterdam: IOS Press.
28. Zhang P, Peng J. SVM vs Regularized Least Squares Classification. Pattern Recognition, International Conference on 2004, 1:176-179.
29. Lingner T, Meinicke P. Fast Target Set Reduction for Large-scale Protein Function Prediction: a Multi-class Multi-label Machine Learning Approach. 8th Workshop on Algorithms in Bioinformatics (WABI) 2008,
30. Walter MC, Rattei T, Arnold R, Güldener U, Münsterkötter M, Nenova K, Kastenmüller G, Tischler P, Wölling A, Volz A, Pongratz N, Jost R, Mewes HW, Frishman D. PEDANT covers all complete RefSeq genomes. Nucleic Acids Res 2009, 37:D408-411. 10.1093/nar/gkn749, 2686588, 18940859.