PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440

BMC Genomics

Volumn 10, Issue SUPPL. 3, 2009, Pages

  Park, Seong Jin ^a   Choi, Jong Soon ^b,c   Kim, Byoung Chul ^a   Jho, Seong Woong ^a   Ryu, Jea Woon ^a   Park, Daeui ^a   Lee, Kyung A ^a   Bhak, Jong ^a   Kim, Seung Il ^b  

^a Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^b Korea Basic Science Institute (KBSI)   (South Korea)

^c Chungnam National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BENZOIC ACID; SUCCINIC ACID; BACTERIAL PROTEIN; PROTEOME;

ARTICLE; BACTERIAL CELL; BACTERIAL METABOLISM; CONTROLLED STUDY; NONHUMAN; PHYSICAL CHEMISTRY; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PSEUDOMONAS PUTIDA; PSEUDOMONAS PUTIDA KT2440; RIBOSOME; CHEMISTRY; COMPUTER PROGRAM; INSTRUMENTATION; INTERNET; METABOLISM; METHODOLOGY; PROTEIN CONFORMATION; PROTEOMICS;

BACTERIA (MICROORGANISMS); PSEUDOMONAS PUTIDA;

BACTERIAL PROTEINS; DATABASES, PROTEIN; INTERNET; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEOME; PROTEOMICS; PSEUDOMONAS PUTIDA; SOFTWARE DESIGN;

ANALYSIS SYSTEM; BIOTECHNOLOGICAL APPLICATIONS; DATABASE SERVICE; DOMAIN-DOMAIN INTERACTIONS; FOREIGN GENES; FUNCTIONAL MODULES; GENE ONTOLOGY; INTERACTION DATABASE; METABOLIC PATHWAYS; MODEL ORGANISMS; PHYSICOCHEMICAL PROPERTY; PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTIONS; PSEUDOMONAS PUTIDA; SELF-INTERACTIONS; SOIL BACTERIUM; SUBNETWORKS;

BACTERIA; METABOLISM; PHYSIOLOGICAL MODELS; PROTEINS;

BIOINFORMATICS;

EID: 71549122280     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-S3-S18     Document Type: Article

References (34)

1. Kim YH, Cho K, Yun SH, Kim JY, Kwon KH, Yoo JS, Kim SI. Analysis of aromatic catabolic pathways in Pseudomonas putida KT 2440 using a combined proteomic approach: 2-DE/MS and cleavable isotope-coded affinity tag analysis. Proteomics 2006, 6(4):1301-1318. 10.1002/pmic.200500329, 16470664.
2. Larimer FW, Chain P, Hauser L, Lamerdin J, Malfatti S, Do L, Land ML, Pelletier DA, Beatty JT, Lang AS. Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat Biotechnol 2004, 22(1):55-61. 10.1038/nbt923, 14704707.
3. Kim WY, Kang S, Kim BC, Oh J, Cho S, Bhak J, Choi JS. SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803. BMC Bioinformatics 2008, 9(Suppl 1):S20. 10.1186/1471-2105-9-S1-S20, 2259421, 18315852.
4. Kim JG, Park D, Kim BC, Cho SW, Kim YT, Park YJ, Cho HJ, Park H, Kim KB, Yoon KO. Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service. BMC Bioinformatics 2008, 9:41. 10.1186/1471-2105-9-41, 2246157, 18215330.
5. Park D, Kim BC, Cho SW, Park SJ, Choi JS, Kim SI, Bhak J, Lee S. MassNet: a functional annotation service for protein mass spectrometry data. Nucleic Acids Res 2008, (36 Web Server):W491-495. 10.1093/nar/gkn241, 2447811, 18448467.
6. Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D. Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol 2004, 5(5):R35. 10.1186/gb-2004-5-5-r35, 416471, 15128449.
7. Brown KR, Jurisica I. Online predicted human interaction database. Bioinformatics 2005, 21(9):2076-2082. 10.1093/bioinformatics/bti273, 15657099.
8. Aragues R, Jaeggi D, Oliva B. PIANA: protein interactions and network analysis. Bioinformatics 2006, 22(8):1015-1017. 10.1093/bioinformatics/btl072, 16510498.
9. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28(1):27-30. 10.1093/nar/28.1.27, 102409, 10592173.
10. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25-29. 10.1038/75556, 10802651.
11. Park J, Lappe M, Teichmann SA. Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. Journal of molecular biology 2001, 307(3):929-938. 10.1006/jmbi.2001.4526, 11273711.
12. Gong S, Yoon G, Jang I, Bolser D, Dafas P, Schroeder M, Choi H, Cho Y, Han K, Lee S. PSIbase: a database of Protein Structural Interactome map (PSIMAP). Bioinformatics (Oxford, England) 2005, 21(10):2541-2543. 10.1093/bioinformatics/bti366, 15749693.
13. 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(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
14. Bader GD, Hogue CW. BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bioinformatics (Oxford, England) 2000, 16(5):465-477. 10.1093/bioinformatics/16.5.465, 10871269.
15. Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D. DIP: the database of interacting proteins. Nucleic acids research 2000, 28(1):289-291. 10.1093/nar/28.1.289, 102387, 10592249.
16. Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A. IntAct: an open source molecular interaction database. Nucleic acids research 2004, (32 Database):D452-455. 10.1093/nar/gkh052, 308786, 14681455.
17. Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G. MINT: a Molecular INTeraction database. FEBS letters 2002, 513(1):135-140. 10.1016/S0014-5793(01)03293-8, 11911893.
18. Peri S, Navarro JD, Kristiansen TZ, Amanchy R, Surendranath V, Muthusamy B, Gandhi TK, Chandrika KN, Deshpande N, Suresh S. Human protein reference database as a discovery resource for proteomics. Nucleic acids research 2004, (32 Database):D497-501. 10.1093/nar/gkh070, 308804, 14681466.
19. Guldener U, Munsterkotter M, Kastenmuller G, Strack N, van Helden J, Lemer C, Richelles J, Wodak SJ, Garcia-Martinez J, Perez-Ortin JE. CYGD: the Comprehensive Yeast Genome Database. Nucleic acids research 2005, (33 Database):D364-368. 540007, 15608217.
20. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID: a general repository for interaction datasets. Nucleic acids research 2006, (34 Database):D535-539. 10.1093/nar/gkj109, 1347471, 16381927.
21. Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. A combined algorithm for genome-wide prediction of protein function. Nature 1999, 402(6757):83-86. 10.1038/47048, 10573421.
22. Walhout AJ, Sordella R, Lu X, Hartley JL, Temple GF, Brasch MA, Thierry-Mieg N, Vidal M. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 2000, 287(5450):116-122. 10.1126/science.287.5450.116, 10615043.
23. Deane CM, Salwinski L, Xenarios I, Eisenberg D. Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics 2002, 1(5):349-356. 10.1074/mcp.M100037-MCP200, 12118076.
24. Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R. Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res 1998, 26(1):320-322. 10.1093/nar/26.1.320, 147209, 9399864.
25. von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B. STRING: a database of predicted functional associations between proteins. Nucleic acids research 2003, 31(1):258-261. 10.1093/nar/gkg034, 165481, 12519996.
26. Chapman B, Chang J. Biopython: Python tools for computational biology. ACM SIGBIO Newsletter 2000, 20(2):15-19.
27. Kall L, Krogh A, Sonnhammer EL. A combined transmembrane topology and signal peptide prediction method. Journal of molecular biology 2004, 338(5):1027-1036. 10.1016/j.jmb.2004.03.016, 15111065.
28. Emanuelsson O, Brunak S, von Heijne G, Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nature protocols 2007, 2(4):953-971. 10.1038/nprot.2007.131, 17446895.
29. Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R. The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic acids research 2004, (32 Database):D262-266. 10.1093/nar/gkh021, 308756, 14681408.
30. Park GW, Kwon KH, Kim JY, Lee JH, Yun SH, Kim SI, Park YM, Cho SY, Paik YK, Yoo JS. Human plasma proteome analysis by reversed sequence database search and molecular weight correlation based on a bacterial proteome analysis. Proteomics 2006, 6(4):1121-1132. 10.1002/pmic.200500318, 16429460.
31. Assenov Y, Ramírez F, Schelhorn SE, Lengauer T, Albrecht M. Computingtopological parameters of biological networks. Bioinformatics 2008, 24(2):282-284. 10.1093/bioinformatics/btm554, 18006545.
32. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5(10):R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
33. Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4:2. 10.1186/1471-2105-4-2, 149346, 12525261.
34. Joy MP, Brock A, Ingber DE, Huang S. High-betweenness proteins in the yeast protein interaction network. J Biomed Biotechnol 2005, 2005(2):96-103. 10.1155/JBB.2005.96, 1184047, 16046814.