How to identify essential genes from molecular networks?

BMC Systems Biology

Volumn 3, Issue , 2009, Pages 102-

  del Rio, Gabriel ^a   Koschützki, Dirk ^b,c   Coello, Gerardo ^a  

^a UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

^b LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

^c FURTWANGEN UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE PROTEIN;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; METABOLISM; PHYSIOLOGY; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; STATISTICAL ANALYSIS; STATISTICAL MODEL;

ALGORITHMS; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; MODELS, BIOLOGICAL; MODELS, STATISTICAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIGNAL TRANSDUCTION;

EID: 70449647110     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-3-102     Document Type: Article

References (34)

1. Wagner A. How to reconstruct a large genetic network from n gene perturbations in fewer than n2 easy steps. Bioinformatics 2001, 17:1183-1197. 10.1093/bioinformatics/17.12.1183, 11751227.
2. Barret CL, Palsson BO. Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach. PLoS Comp Biol 2006, 2:e52.
3. Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 2001, 292:929-934. 10.1126/science.292.5518.929, 11340206.
4. Lee I, Li Z, Marcotte EM. An Improved, Bias-Reduced Probabilistic Functional Gene Network of Baker's Yeast, Saccharomyces cerevisiae. PLoS ONE 2007, 2:e988. 10.1371/journal.pone.0000988, 1991590, 17912365.
5. Gerdes S, Edwards R, Kubal M, Fonstein M, Stevens R, Osterman A. Essential genes on metabolic maps. Curr Opin Biotechnol 2006, 17:448-56. 10.1016/j.copbio.2006.08.006, 16978855.
6. Förster J, Famili I, Palsson BO, Nielsen J. Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. OMICS 2003, 7:193-202. 10.1089/153623103322246584, 14506848.
7. Wunderlich Z, Mirny LA. Using the topology of metabolic networks to predict viability of mutant strains. Biophys J 2006, 91:2304-2311. 10.1529/biophysj.105.080572, 1557581, 16782788.
8. Becker SA, Palsson BO. Three factors underlying incorrect in silico predictions of essential metabolic genes. BMC Syst Biol 2008, 2:14. 10.1186/1752-0509-2-14, 2248557, 18248675.
9. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, 34:D354-D357. 10.1093/nar/gkj102, 1347464, 16381885.
10. Duarte NC, Herrgård MJ, Palsson B. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 2004, 14:1298-1309. 10.1101/gr.2250904, 442145, 15197165.
11. Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 2003, 34:167-177.
12. Kuhn KM, DeRisi JL, Brown PO, Sarnow P. Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol Cell Biol 2001, 21:916-917. 10.1128/MCB.21.3.916-927.2001, 86682, 11154278.
13. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabási AL. The large-scale organization of metabolic networks. Nature 2000, 407:651-654. 10.1038/35036627, 11034217.
14. Ma HW, Zeng AP. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 2003, 19:270-277. 10.1093/bioinformatics/19.2.270, 12538249.
15. Ma HW, Zeng AP. The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 2003, 19:1423-1430. 10.1093/bioinformatics/btg177, 12874056.
16. Junker BH, Koschützi D, Schreiber F. Exploration of biological network centralities with CentiBiN. BMC Bioinformatics 2006, 7:219. 10.1186/1471-2105-7-219, 1524990, 16630347.
17. Koschützki D, Lehmann KA, Peeters L, Richter S, Tenfelde-Podehl D, Zlotowski O. Centrality Indices. Network Analysis: Methodological Foundations 2005, 16-61. LNCS 3418 Springer, Brandes U, Erlebach T.
18. Thibert B, Bredesen DE, del Rio G. Improved prediction of critical residues for protein function based on network and phylogenetic analyses. BMC Bioinformatics 2005, 6:213. 10.1186/1471-2105-6-213, 1208857, 16124876.
19. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, Chu AM, Connelly C, Davis K, Dietrich F, Dow SW, El Bakkoury M, Foury F, Friend SH, Gentalen E, Giaever G, Hegemann JH, Jones T, Laub M, Liao H, Liebundguth N, Lockhart DJ, Lucau-Danila A, Lussier M, M'Rabet N, Menard P, Mittmann M, Pai C, Rebischung C, Revuelta JL, Riles L, Roberts CJ, Ross-MacDonald P, Scherens B, Snyder M, Sookhai-Mahadeo S, Storms RK, Véronneau S, Voet M, Volckaert G, Ward TR, Wysocki R, Yen GS, Yu K, Zimmermann K, Philippsen P, Johnston M, Davis RW. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 1999, 285:901-906. 10.1126/science.285.5429.901, 10436161.
20. Hanley JA, McNeil BJ. The meaning and use of the area under a Receiver Operating Characteristic (ROC) curve. Radiology 1982, 143:29-36.
21. Zotenko E, Mestre J, O'Leary DP, Przytycka TM. Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Comput Biol 2008, 4:e1000140. 10.1371/journal.pcbi.1000140, 2467474, 18670624.
22. 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, 25:25-29. 10.1038/75556, 10802651.
23. Familii I, Forster J, Nielsen J, Palsson BO. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc Natl Acad Sci USA 2003, 100:13134-13139. 10.1073/pnas.2235812100, 263729, 14578455.
24. Vilela M, Borges CC, Vinga S, Vasconcelos AT, Santos H, Voit EO, Almeida JS. Automated smoother for the numerical decoupling of dynamics models. BMC Bioinformatics 2007, 8:305. 10.1186/1471-2105-8-305, 2041957, 17711581.
25. Mahadevan R, Palsson BO. Properties of metabolic networks: structure versus function. Biophys J 2005, 88:L07-L09. 10.1529/biophysj.104.055723, 1305059, 15574705.
26. Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 2007, 3:e59. 10.1371/journal.pcbi.0030059, 1853125,1853125, 17447836.
27. Estrada E. Protein bipartivity and essentiality in the yeast protein-protein interaction network. J Proteome Res 2006, 5:2177-84. 10.1021/pr060106e, 16944929.
28. He X, Zhang J. Why do hubs tend to be essential in protein networks?. PLoS Genet 2006, 2:e88. 10.1371/journal.pgen.0020088, 1473040,1473040, 16751849.
29. Estrada E. Virtual identification of essential proteins within the protein interaction network of yeast. Proteomics 2006, 6:35-40. 10.1002/pmic.200500209, 16281187.
30. Wachi S, Yoneda K, Wu R. Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics 2005, 21:4205-4208. 10.1093/bioinformatics/bti688, 16188928.
31. Joy MP, Brock A, Ingber DE, Huang S. High-betweenness proteins in the yeast protein interaction network. J Biomed Biotechnol 2005, 2005:96-103. 10.1155/JBB.2005.96, 1184047, 16046814.
32. Hahn MW, Kern AD. Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 2005, 22:803-806. 10.1093/molbev/msi072, 15616139.
33. Kuepfer L, Sauer U, Blank LM. Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Research 2005, 15:1421-1430. 10.1101/gr.3992505, 1240085, 16204195.
34. Papp B, Pál P, Hurst LD. Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 2004, 429:661-664. 10.1038/nature02636, 15190353.