DBMLoc: A Database of proteins with multiple subcellular localizations

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Zhang, Song ^a   Xia, Xuefeng ^a   Shen, Jincheng ^a   Zhou, Yun ^a   Sun, Zhirong ^a  

^a TSINGHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

HIERARCHICAL ARCHITECTURES; KEY FEATURE; PROTEIN DATABASE; PROTEIN FUNCTIONS; PROTEIN-PROTEIN INTERACTIONS; SUB-CELLULAR; SUBCELLULAR COMPARTMENTS; SUBCELLULAR LOCALIZATIONS;

DATABASE SYSTEMS;

PROTEINS;

AMINO ACID SEQUENCE; ARTICLE; CELL MEMBRANE; CELL NUCLEUS; CELLULAR DISTRIBUTION; CYTOPLASM; DBMLOC DATABASE; ENDOPLASMIC RETICULUM; HUMAN; NONHUMAN; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN INTERACTION; PROTEIN LOCALIZATION; PROTEIN SECRETION; SWISS-PROT; CELL FRACTIONATION; CLASSIFICATION; COMPUTER INTERFACE; DATA BASE; INFORMATION RETRIEVAL; METABOLISM; METHODOLOGY;

PROTEIN;

DATABASE MANAGEMENT SYSTEMS; DATABASES, PROTEIN; INFORMATION STORAGE AND RETRIEVAL; PROTEINS; SUBCELLULAR FRACTIONS; USER-COMPUTER INTERFACE;

EID: 42149083808     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-127     Document Type: Article

References (25)

1. Huh WK Falvo JV Gerke LC Carroll AS Howson RW Weissman JS O'Shea EK Global analysis of protein localization in budding yeast Nature 2003, 425(6959):686-691. 10.1038/nature02026 14562095
2. Kumar A Agarwal S Heyman JA Matson S Heidtman M Piccirillo S Umansky L Drawid A Jansen R Liu Y Cheung KH Miller P Gerstein M Roeder GS Snyder M Subcellular localization of the yeast proteome Genes Dev 2002, 16(6):707-719. 155358 11914276 10.1101/gad.970902
3. Ross-Macdonald P Coelho PS Roemer T Agarwal S Kumar A Jansen R Cheung KH Sheehan A Symoniatis D Umansky L Heidtman M Nelson FK Iwasaki H Hager K Gerstein M Miller P Roeder GS Snyder M Large-scale analysis of the yeast genome by transposon tagging and gene disruption Nature 1999, 402(6760):413-418. 10.1038/46558 10586881
4. Fink JL Aturaliya RN Davis MJ Zhang F Hanson K Teasdale MS Kai C Kawai J Carninci P Hayashizaki Y Teasdale RD LOCATE: A mouse protein subcellular localization database Nucleic Acids Res 2006, 34: Database issue D213-7. 1347432 16381849 10.1093/nar/gkj069
5. Wiwatwattana N Kumar A Organelle DB: A cross-species database of protein localization and function Nucleic Acids Res 2005, 33: Database issue D598-604. 540025 15608270 10.1093/nar/gki071
6. Guo T Hua S Ji X Sun Z DBSubLoc: Database of protein subcellular localization Nucleic Acids Res 2004, 32: Database issue D122-4. 308843 14681374 10.1093/nar/gkh109
7. Nair R Rost B LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets Nucleic Acids Res 2004, 32: Web Server issue W517-21. 441579 15215440 10.1093/nar/gkh441
8. Lu P Szafron D Greiner R Wishart DS Fyshe A Pearcy B Poulin B Eisner R Ngo D Lamb N PA-GOSUB: A searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization Nucleic Acids Res 2005, 33: Database issue D147-53. 540074 15608166 10.1093/nar/gki120
9. Rey S Acab M Gardy JL Laird MR deFays K Lambert C Brinkman FS PSORTdb: A protein subcellular localization database for bacteria Nucleic Acids Res 2005, 33: Database issue D164-8. 539981 15608169 10.1093/nar/gki027
10. Pierleoni A Martelli PL Fariselli P Casadio R eSLDB: Eukaryotic subcellular localization database Nucleic Acids Res 2007, 35: Database issue D208-12. 1669738 17108361 10.1093/nar/gkl775
11. Nielsen H Engelbrecht J Brunak S von Heijne G A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites Int J Neural Syst 1997, 8(5-6):581-599. 10.1142/S0129065797000537 10065837
12. Mott R Schultz J Bork P Ponting CP Predicting protein cellular localization using a domain projection method Genome Res 2002, 12(8):1168-1174. 186639 12176924 10.1101/gr.96802
13. Gardy JL Spencer C Wang K Ester M Tusnady GE Simon I Hua S deFays K Lambert C Nakai K Brinkman FS PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria Nucleic Acids Res 2003, 31(13):3613-3617. 169008 12824378 10.1093/nar/gkg602
14. Hua S Sun Z Support vector machine approach for protein subcellular localization prediction Bioinformatics 2001, 17(8):721-728. 10.1093/ bioinformatics/17.8.721 11524373
15. Reinhardt A Hubbard T Using neural networks for prediction of the subcellular location of proteins Nucleic Acids Res 1998, 26(9):2230-2236. 147531 9547285 10.1093/nar/26.9.2230
16. Sarda D Chua GH Li KB Krishnan A pSLIP: SVM based protein subcellular localization prediction using multiple physicochemical properties BMC Bioinformatics 2005, 6:152. 1182350 15963230 10.1186/1471-2105-6-152
17. Foster LJ de Hoog CL Zhang Y Zhang Y Xie X Mootha VK Mann M A mammalian organelle map by protein correlation profiling Cell 2006, 125(1):187-199. 10.1016/j.cell.2006.03.022 16615899
18. Boeckmann B Bairoch A Apweiler R Blatter MC Estreicher A Gasteiger E Martin MJ Michoud K O'Donovan C Phan I Pilbout S Schneider M The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Nucleic Acids Res 2003, 31(1):365-370. 165542 12520024 10.1093/nar/gkg095
19. Cotter D Guda P Fahy E Subramaniam S MitoProteome: Mitochondrial protein sequence database and annotation system Nucleic Acids Res 2004, 32: Database issue D463-7. 308782 14681458 10.1093/nar/gkh048
20. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Harris MA Hill DP Issel-Tarver L Kasarskis A Lewis S Matese JC Richardson JE Ringwald M Rubin GM Sherlock G Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000, 25(1):25-29. 10.1038/75556 10802651
21. 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 Res 2004, 32: Database issue D262-6. 308756 14681408 10.1093/nar/gkh021
22. Wheeler DL Chappey C Lash AE Leipe DD Madden TL Schuler GD Tatusova TA Rapp BA Database resources of the National Center for Biotechnology Information Nucleic Acids Res 2000, 28(1):10-14. 102437 10592169 10.1093/ nar/28.1.10
23. Xenarios I Rice DW Salwinski L Baron MK Marcotte EM Eisenberg D DIP: The database of interacting proteins Nucleic Acids Res 2000, 28(1):289-291. 102387 10592249 10.1093/nar/28.1.289
24. Zanzoni A Montecchi-Palazzi L Quondam M Ausiello G Helmer-Citterich M Cesareni G MINT: A Molecular INTeraction database FEBS Lett 2002, 513(1):135-140. 10.1016/S0014-5793(01)03293-8 11911893
25. Bader GD Betel D Hogue CW BIND: The Biomolecular Interaction Network Database Nucleic Acids Res 2003, 31(1):248-250. 165503 12519993 10.1093/ nar/gkg056