Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets

Plant Cell

Volumn 22, Issue 4, 2010, Pages 997-1005

  Lee, KiYoung ^a,b   Thorneycroft, David ^c   Achuthan, Premanand ^c   Hermjakob, Henning ^c   Ideker, Trey ^b  

^a Ajou University School of Medicine   (South Korea)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 77953224209     PISSN: 10404651     EISSN: 1532298X     Source Type: Journal    
DOI: 10.1105/tpc.109.072736     Document Type: Article

References (39)

1. Aranda, B., et al. (2010). The IntAct molecular interaction database in 2010. Nucleic Acids Res. 38: D525-D531.
2. Brady, S.M., and Provart, N.J. (2009). Web-queryable large-scale data sets for hypothesis generation in plant biology. Plant Cell 21: 1034-1051.
3. Breitkreutz, B.J., Stark, C., Reguly, T., Boucher, L., Breitkreutz, A., Livstone, M., Oughtred, R., Lackner, D.H., Bahler, J., Wood, V., Dolinski, K., and Tyers, M. (2008). The BioGRID Interaction Data-base: 2008 update. Nucleic Acids Res. 36: D637-D640.
4. Brown, J.W., Shaw, P.J., Shaw, P., and Marshall, D.F. (2005). Arabidopsis nucleolar protein database (AtNoPDB). Nucleic Acids Res. 33: D633-D636.
5. Cline, M.S., et al. (2007). Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc. 2: 2366-2382.
6. Cui, J., Li, P., Li, G., Xu, F., Zhao, C., Li, Y., Yang, Z., Wang, G., Yu, Q., Li, Y., and Shi, T. (2008). AtPID: Arabidopsis thaliana protein interactome database-an integrative platform for plant systems biology. Nucleic Acids Res. 36: D999-D1008.
7. Cusick, M.E., et al. (2009a). Literature-curated protein interaction datasets. Nat. Methods 6: 39-46.
8. Cusick, M.E., et al. (2009b). Addendum: Literature-curated protein interaction datasets. Nat. Methods 6: 934-935.
9. De Bodt, S., Proost, S., Vandepoele, K., Rouze, P., and Van de Peer, Y. (2009). Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics 10: 288.
10. Eubel, H., Meyer, E.H., Taylor, N.L., Bussell, J.D., O'Toole, N., Heazlewood, J.L., Castleden, I., Small, I.D., Smith, S.M., and Millar, A.H. (2008). Novel proteins, putative membrane transporters, and an integrated metabolic network are revealed by quantitative proteomic analysis of Arabidopsis cell culture peroxisomes. Plant Physiol. 148: 1809-1829.
11. Fukushima, A., Kusano, M., Redestig, H., Arita, M., and Saito, K. (2009). Integrated omics approaches in plant systems biology. Curr. Opin. Chem. Biol. 13: 532-538.
12. Geisler-Lee, J., O'Toole, N., Ammar, R., Provart, N.J., Millar, A.H., and Geisler, M. (2007). A predicted interactome for Arabidopsis. Plant Physiol. 145: 317-329.
13. Heazlewood, J.L., Verboom, R.E., Tonti-Filippini, J., Small, I., and Millar, A.H. (2007). SUBA: The Arabidopsis Subcellular Database. Nucleic Acids Res. 35: D213-D218.
14. Jorrin, J.V., Maldonado, A.M., and Castillejo, M.A. (2007). Plant proteome analysis: A 2006 update. Proteomics 7: 2947-2962.
15. Kabiljo, R., Clegg, A.B., and Shepherd, A.J. (2009). A realistic assessment of methods for extracting gene/protein interactions from free text. BMC Bioinformatics 10: 233.
16. Laloi, C., Rayapuram, N., Chartier, Y., Grienenberger, J.M., Bonnard, G., and Meyer, Y. (2001). Identification and characterization of a mitochondrial thioredoxin system in plants. Proc. Natl. Acad. Sci. USA 98: 14144-14149.
17. Lee, C.P., Eubel, H., O'Toole, N., and Millar, A.H. (2008). Heterogeneity of the mitochondrial proteome for photosynthetic and non-photosynthetic Arabidopsis metabolism. Mol. Cell. Proteomics 7: 1297-1316.
18. Lee, K., Chuang, H.Y., Beyer, A., Sung, M.K., Huh, W.K., Lee, B., and Ideker, T. (2008). Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Res. 36: e136.
19. Lin, M., Hu, B., Chen, L., Sun, P., Fan, Y., Wu, P., and Chen, X. (2009). Computational identification of potential molecular interactions in Arabidopsis. Plant Physiol. 151: 34-46
20. Lysenko, A., Hindle, M.M., Taubert, J., Saqi, M., and Rawlings, C.J. (2009). Data integration for plant genomics-exemplars from the integration of Arabidopsis thaliana databases. Brief. Bioinform. 10: 676-693.
21. Maere, S., Heymans, K., and Kuiper, M. (2005). BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21: 3448-3449.
22. Maes, L., Inze, D., and Goossens, A. (2008). Functional specialization of the TRANSPARENT TESTA GLABRA1 network allows differential hormonal control of laminal and marginal trichome initiation in Arabidopsis rosette leaves. Plant Physiol. 148: 1453-1464.
23. Millar, A.H., Carrie, C., Pogson, B., and Whelan, J. (2009). Exploring the function-location nexus: Using multiple lines of evidence in defining the subcellular location of plant proteins. Plant Cell 21: 1625-1631.
24. Molodianovitch, K., Faraggi, D., and Reiser, B. (2006). Comparing the areas under two correlated ROC curves: Parametric and non-parametric approaches. Biom. J. 48: 745-757.
25. Morsy, M., Gouthu, S., Orchard, S., Thorneycroft, D., Harper, J.F., Mittler, R., and Cushman, J.C. (2008). Charting plant interactomes: Possibilities and challenges. Trends Plant Sci. 13: 183-191.
26. Orchard, S., Kerrien, S., Jones, P., Ceol, A., Chatr-Aryamontri, A., Salwinski, L., Nerothin, J., and Hermjakob, H. (2007). Submit your interaction data the IMEx way: A step by step guide to trouble-free deposition. Proteomics 7(Suppl 1): 28-34.
27. Orchard, S., and Taylor, C.F. (2009). Debunking minimum information myths: One hat need not fit all. N. Biotechnol 25: 171-172.
28. Poole, R.L. (2007). The TAIR database. Methods Mol. Biol. 406: 179-212.
29. Reumann, S., Ma, C., Lemke, S., and Babujee, L. (2004). AraPerox. A database of putative Arabidopsis proteins from plant peroxisomes. Plant Physiol. 136: 2587-2608.
30. Rhee, S.Y., Wood, V., Dolinski, K., and Draghici, S. (2008). Use and misuse of the gene ontology annotations. Nat. Rev. Genet. 9: 509-515.
31. Rodriguez, H., et al. (2009). Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: The Amsterdam principles. J Proteome Res. 8: 3689-3692.
32. Salwinski, L., et al. (2009). Recurated protein interaction datasets. Nat. Methods 6: 860-861.
33. Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13: 2498-2504.
34. Stein, A., Pache, R.A., Bernado, P., Pons, M., and Aloy, P. (2009). Dynamic interactions of proteins in complex networks: A more structured view. FEBS J. 276: 5390-5405.
35. Streiner, D.L., and Cairney, J. (2007). What's under the ROC? An introduction to receiver operating characteristics curves. Can. J. Psychiatry 52: 121-128.
36. Suderman, M., and Hallett, M. (2007). Tools for visually exploring biological networks. Bioinformatics 23: 2651-2659.
37. Uhrig, J.F. (2006). Protein interaction networks in plants. Planta 224: 771-781.
38. Winnenburg, R., Wachter, T., Plake, C., Doms, A., and Schroeder, M. (2008). Facts from text: Can text mining help to scale-up high-quality manual curation of gene products with ontologies? Brief. Bioinform. 9: 466-478.
39. Yu, J., and Finley, R.L., Jr. (2009). Combining multiple positive training sets to generate confidence scores for protein-protein interactions. Bioinformatics 25: 105-111.