Metagenomic annotation networks: Construction and applications

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  Vey, Gregory ^a   Moreno Hagelsieb, Gabriel ^b  

^a UNIVERSITY OF WATERLOO   (Canada)

^b WILFRID LAURIER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOCATALYST; GENE FUNCTION; GENE INTERACTION; GENE STRUCTURE; HUMAN; INTERMETHOD COMPARISON; METAGENOMIC ANNOTATION NETWORK; METAGENOMICS; MICROBIAL COMMUNITY; OPERON; PREDICTION; TAXONOMY;

ANIMALS; CELLULASE; GASTROINTESTINAL TRACT; GENE REGULATORY NETWORKS; GENETIC VARIATION; HUMANS; METAGENOME; METAGENOMICS; MOLECULAR SEQUENCE ANNOTATION; SUS SCROFA;

EID: 84864683903     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0041283     Document Type: Article

References (37)

1. Leinonen R, Sugawara H, Shumway M, (2011) International Nucleotide Sequence Database C. The sequence read archive. Nucleic Acids Res 39: D19-21.
2. Kodama Y, Shumway M, Leinonen R, (2012) International Nucleotide Sequence Database C. The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res 40: D54-56.
3. Wooley JC, Godzik A, Friedberg I, (2010) A primer on metagenomics. PLoS computational biology 6: e1000667.
4. Ferrer M, Martinez-Abarca F, Golyshin PN, (2005) Mining genomes and 'metagenomes' for novel catalysts. Curr Opin Biotechnol 16: 588-593.
5. Tringe SG, Rubin EM, (2005) Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 6: 805-814.
6. Pignatelli M, Aparicio G, Blanquer I, Hernandez V, Moya A, et al. (2008) Metagenomics reveals our incomplete knowledge of global diversity. Bioinformatics 24: 2124-2125.
7. Janga SC, Diaz-Mejia JJ, Moreno-Hagelsieb G, (2011) Network-based function prediction and interactomics: the case for metabolic enzymes. Metab Eng 13: 1-10.
8. Sun MG, Kim PM, (2011) Evolution of biological interaction networks: from models to real data. Genome Biol 12: 235.
9. Peregrin-Alvarez JM, Xiong X, Su C, Parkinson J, (2009) The Modular Organization of Protein Interactions in Escherichia coli. PLoS computational biology 5: e1000523.
10. Hsu JT, Peng CH, Hsieh WP, Lan CY, Tang CY, (2011) A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle. BMC Bioinformatics 12: 281.
11. Liu B, Pop M, (2011) MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets. BMC Proc 5 Suppl 2: S9.
12. Konietzny SG, Dietz L, McHardy AC, (2011) Inferring functional modules of protein families with probabilistic topic models. BMC Bioinformatics 12: 141.
13. Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, et al. (2008) IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res 36: D534-538.
14. Chen GJ, Russell JB, (1989) Sodium-dependent transport of branched-chain amino acids by a monensin-sensitive ruminal peptostreptococcus. Appl Environ Microbiol 55: 2658-2663.
15. Nataf Y, Yaron S, Stahl F, Lamed R, Bayer EA, et al. (2009) Cellodextrin and laminaribiose ABC transporters in Clostridium thermocellum. J Bacteriol 191: 203-209.
16. Lykidis A, Mavromatis K, Ivanova N, Anderson I, Land M, et al. (2007) Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. J Bacteriol 189: 2477-2486.
17. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-1359.
18. Kaddurah-Daouk R, Baillie RA, Zhu H, Zeng ZB, Wiest MM, et al. (2011) Enteric microbiome metabolites correlate with response to simvastatin treatment. PLoS One 6: e25482.
19. Kidd P, Head K, (2005) A review of the bioavailability and clinical efficacy of milk thistle phytosome: a silybin-phosphatidylcholine complex (Siliphos). Altern Med Rev 10: 193-203.
20. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, et al. (2008) Functional metagenomic profiling of nine biomes. Nature 452: 629-632.
21. Manichanh C, Reeder J, Gibert P, Varela E, Llopis M, et al. (2010) Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Genome Res 20: 1411-1419.
22. Aravind L, (2000) Guilt by association: contextual information in genome analysis. Genome Res 10: 1074-1077.
23. Li LL, Taghavi S, McCorkle SM, Zhang YB, Blewitt MG, et al. (2011) Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases. Biotechnol Biofuels 4: 23.
24. Candela M, Maccaferri S, Turroni S, Carnevali P, Brigidi P, (2010) Functional intestinal microbiome, new frontiers in prebiotic design. Int J Food Microbiol 140: 93-101.
25. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, et al. (2005) Comparative metagenomics of microbial communities. Science 308: 554-557.
26. Rende D, Baysal N, Kirdar B, (2011) A novel integrative network approach to understand the interplay between cardiovascular disease and other complex disorders. Mol Biosyst 7: 2205-2219.
27. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480-484.
28. Finegold SM, Dowd SE, Gontcharova V, Liu C, Henley KE, et al. (2010) Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe 16: 444-453.
29. Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muniz-Rascado L, et al. (2011) RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic acids research 39: D98-105.
30. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, et al. (2008) The metagenomics RAST server- a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
31. Salgado H, Moreno-Hagelsieb G, Smith TF, Collado-Vides J, (2000) Operons in Escherichia coli: genomic analyses and predictions. Proc Natl Acad Sci U S A 97: 6652-6657.
32. Moreno-Hagelsieb G, Collado-Vides J, (2002) A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics 18 Suppl 1: S329-336.
33. Vey G, Moreno-Hagelsieb G, (2010) Beyond the bounds of orthology: functional inference from metagenomic context. Mol Biosyst 6: 1247-1254.
34. Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, et al. (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 40: D742-753.
35. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41.
36. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M, (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40: D109-114.
37. Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, et al. (2007) TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res 35: D260-264.