Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N: Towards a proteome-scale map of the human protein-protein interaction network. Nature. 2005, 437 (7062): 1173-1178.
Article
CAS
PubMed
Google Scholar
Lehner B, Fraser AG: A first-draft human protein-interaction map. Genome Biol. 2004, 5 (9): R63-
Article
PubMed Central
PubMed
Google Scholar
Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S: A human protein-protein interaction network: a resource for annotating the proteome. Cell. 2005, 122 (6): 957-968.
Article
CAS
PubMed
Google Scholar
Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, Kalyana-Sundaram S, Ghosh D, Pandey A, Chinnaiyan AM: Probabilistic model of the human protein-protein interaction network. Nat Biotechnol. 2005, 23 (8): 951-959.
Article
CAS
PubMed
Google Scholar
Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E: A protein interaction map of Drosophila melanogaster. Science. 2003, 302 (5651): 1727-1736.
Article
CAS
PubMed
Google Scholar
Formstecher E, Aresta S, Collura V, Hamburger A, Meil A, Trehin A, Reverdy C, Betin V, Maire S, Brun C: Protein interaction mapping: a Drosophila case study. Genome Res. 2005, 15 (3): 376-384.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y: A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A. 2001, 98 (8): 4569-4574.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ho E, Webber R, Wilkins MR: Interactive three-dimensional visualization and contextual analysis of protein interaction networks. J Proteome Res. 2008, 7 (1): 104-112.
Article
CAS
PubMed
Google Scholar
Gavin IM, Kukhtin A, Glesne D, Schabacker D, Chandler DP: Analysis of protein interaction and function with a 3-dimensional MALDI-MS protein array. Biotechniques. 2005, 39 (1): 99-107.
Article
CAS
PubMed
Google Scholar
Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T: A map of the interactome network of the metazoan C. elegans. Science. 2004, 303 (5657): 540-543.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B: Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet. 2006, 38 (3): 285-293.
Article
CAS
PubMed
Google Scholar
Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S: Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science. 2008, 320 (5878): 938-941.
Article
CAS
PubMed
Google Scholar
Geisler-Lee J, O'Toole N, Ammar R, Provart NJ, Millar AH, Geisler M: A predicted interactome for Arabidopsis. Plant Physiol. 2007, 145 (2): 317-329.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bhardwaj N, Lu H: Correlation between gene expression profiles and protein-protein interactions within and across genomes. Bioinformatics. 2005, 21 (11): 2730-2738.
Article
CAS
PubMed
Google Scholar
Date SV, Stoeckert CJ: Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale. Genome Res. 2006, 16 (4): 542-549.
Article
PubMed Central
CAS
PubMed
Google Scholar
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-
Article
PubMed Central
PubMed
Google Scholar
Lin M, Hu B, Chen L, Sun P, Fan Y, Wu P, Chen X: Computational Identification of Potential Molecular Interactions in Arabidopsis Thaliana. Plant Physiol. 2009
Google Scholar
Sun J, Sun Y, Ding G, Liu Q, Wang C, He Y, Shi T, Li Y, Zhao Z: InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes. BMC Bioinformatics. 2007, 8: 414-
Article
PubMed Central
PubMed
Google Scholar
Chen Y, Xu D: Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. Nucleic Acids Res. 2004, 32 (21): 6414-6424.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Shi T: AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology. Nucleic Acids Res. 2008, 36 (Database issue): D999-1008.
PubMed Central
CAS
PubMed
Google Scholar
Masoudi-Nejad A, Goto S, Endo TR, Kanehisa M: KEGG bioinformatics resource for plant genomics research. Methods Mol Biol. 2007, 406: 437-458.
CAS
PubMed
Google Scholar
Ogata H, Goto S, Fujibuchi W, Kanehisa M: Computation with the KEGG pathway database. Biosystems. 1998, 47 (1-2): 119-128.
Article
CAS
PubMed
Google Scholar
Mueller LA, Zhang P, Rhee SY: AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol. 2003, 132 (2): 453-460.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhang P, Foerster H, Tissier CP, Mueller L, Paley S, Karp PD, Rhee SY: MetaCyc and AraCyc. Metabolic pathway databases for plant research. Plant Physiol. 2005, 138 (1): 27-37.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R: IntAct--open source resource for molecular interaction data. Nucleic Acids Res. 2007, 35 (Database issue): D561-565.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bader GD, Betel D, Hogue CW: BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 2003, 31 (1): 248-250.
Article
PubMed Central
CAS
PubMed
Google Scholar
Willis RC, Hogue CW: Searching, viewing, and visualizing data in the Biomolecular Interaction Network Database (BIND). Curr Protoc Bioinformatics. 2006, Chapter 8 (Unit 8): 9-
PubMed
Google Scholar
Poole RL: The TAIR database. Methods Mol Biol. 2007, 406: 179-212.
CAS
PubMed
Google Scholar
Ort DR, Grennan AK: Plant Physiology and TAIR partnership. Plant Physiol. 2008, 146 (3): 1022-1023.
Article
PubMed Central
CAS
PubMed
Google Scholar
Van Calster B, Nabney I, Timmerman D, Van Huffel S: The Bayesian approach: a natural framework for statistical modeling. Ultrasound Obstet Gynecol. 2007, 29 (5): 485-488.
Article
CAS
PubMed
Google Scholar
Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M: A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science. 2003, 302 (5644): 449-453.
Article
CAS
PubMed
Google Scholar
Vazquez A, Flammini A, Maritan A, Vespignani A: Global protein function prediction from protein-protein interaction networks. Nat Biotechnol. 2003, 21 (6): 697-700.
Article
CAS
PubMed
Google Scholar
Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A: Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 2006, 16 (5): 686-691.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B: Proteome survey reveals modularity of the yeast cell machinery. Nature. 2006, 440 (7084): 631-636.
Article
CAS
PubMed
Google Scholar
Ohi MD, Link AJ, Ren L, Jennings JL, McDonald WH, Gould KL: Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs. Mol Cell Biol. 2002, 22 (7): 2011-2024.
Article
PubMed Central
CAS
PubMed
Google Scholar
Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization. Nat Rev Genet. 2004, 5 (2): 101-113.
Article
CAS
PubMed
Google Scholar
Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S: AmiGO: online access to ontology and annotation data. Bioinformatics. 2008
Google Scholar
Mentzen WI, Peng J, Ransom N, Nikolau BJ, Wurtele ES: Articulation of three core metabolic processes in Arabidopsis: fatty acid biosynthesis, leucine catabolism and starch metabolism. BMC Plant Biol. 2008, 8: 76-
Article
PubMed Central
PubMed
Google Scholar
Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2004, 32 (Database issue): D449-451.
Article
PubMed Central
CAS
PubMed
Google Scholar
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.
Article
PubMed Central
CAS
PubMed
Google Scholar
Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D: DIP: The Database of Interacting Proteins: 2001 update. Nucleic Acids Res. 2001, 29 (1): 239-241.
Article
PubMed Central
CAS
PubMed
Google Scholar
Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, Eisenberg D: DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 2002, 30 (1): 303-305.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ostlund G, Schmitt T, Forslund K, Kostler T, Messina DN, Roopra S, Frings O, Sonnhammer EL: InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res. 2010, 38 (Database issue): D196-203.
Article
PubMed Central
PubMed
Google Scholar
Berglund AC, Sjolund E, Ostlund G, Sonnhammer EL: InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res. 2008, 36 (Database issue): D263-266.
PubMed Central
CAS
PubMed
Google Scholar
O'Brien KP, Remm M, Sonnhammer EL: Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res. 2005, 33 (Database issue): D476-480.
Article
PubMed Central
PubMed
Google Scholar
Becker RA, Chambers JM, Wilks AR: The New S Language. Wadsworth & Brooks/Cole. 1988
Google Scholar