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Volumn 7, Issue MAR, 2016, Pages

Predicting essential genes and proteins based on machine learning and network topological features: A comprehensive review

Author keywords

Essential genes proteins; Machine learning; Network topological features; Prediction models; Systems biology

Indexed keywords

PROTEIN;

EID: 84964679066     PISSN: None     EISSN: 1664042X     Source Type: Journal    
DOI: 10.3389/fphys.2016.00075     Document Type: Review
Times cited : (76)

References (59)
  • 1
    • 70449369491 scopus 로고    scopus 로고
    • Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information
    • Acencio, M. L., and Lemke, N. (2009). Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information. BMC Bioinformatics 10:290. doi: 10.1186/1471-2105-10-290
    • (2009) BMC Bioinformatics , vol.10 , pp. 290
    • Acencio, M.L.1    Lemke, N.2
  • 2
    • 17844405878 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation
    • Becker, S. A., and Palsson, B. Ø. (2005). Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiol. 5:8. doi: 10.1186/1471-2180-5-8
    • (2005) BMC Microbiol , vol.5 , pp. 8
    • Becker, S.A.1    Palsson, B.Ø.2
  • 3
    • 84936824655 scopus 로고
    • Power and centrality: a family of measures
    • Bonacich, P. (1987). Power and centrality: a family of measures. Am. J. Sociol. 92, 1170-1182. doi: 10.1086/228631
    • (1987) Am. J. Sociol , vol.92 , pp. 1170-1182
    • Bonacich, P.1
  • 4
    • 84922460388 scopus 로고    scopus 로고
    • Identifying essential Streptococcus sanguinis genes using genome-wide deletion mutation
    • Chen, L., Ge, X., and Xu, P. (2015). Identifying essential Streptococcus sanguinis genes using genome-wide deletion mutation. Methods Mol. Biol. 1279, 15-23. doi: 10.1007/978-1-4939-2398-4_2
    • (2015) Methods Mol. Biol , vol.1279 , pp. 15-23
    • Chen, L.1    Ge, X.2    Xu, P.3
  • 5
    • 84862165032 scopus 로고    scopus 로고
    • OGEE: an online gene essentiality database
    • Chen, W. H., Minguez, P., Lercher, M. J., and Bork, P. (2012). OGEE: an online gene essentiality database. Nucleic Acids Res. 40, D901-D906. doi: 10.1093/nar/gkr986
    • (2012) Nucleic Acids Res , vol.40 , pp. D901-D906
    • Chen, W.H.1    Minguez, P.2    Lercher, M.J.3    Bork, P.4
  • 6
    • 15844364199 scopus 로고    scopus 로고
    • Understanding protein dispensability through machine-learning analysis of high-throughput data
    • Chen, Y., and Xu, D. (2005). Understanding protein dispensability through machine-learning analysis of high-throughput data. Bioinformatics 21, 575-581. doi: 10.1093/bioinformatics/bti058
    • (2005) Bioinformatics , vol.21 , pp. 575-581
    • Chen, Y.1    Xu, D.2
  • 7
    • 84890541602 scopus 로고    scopus 로고
    • A new computational strategy for predicting essential genes
    • Cheng, J., Wu, W., Zhang, Y., Li, X., Jiang, X., Wei, G., et al. (2013). A new computational strategy for predicting essential genes. BMC Genomics 14:910. doi: 10.1186/1471-2164-14-910
    • (2013) BMC Genomics , vol.14 , pp. 910
    • Cheng, J.1    Wu, W.2    Zhang, Y.3    Li, X.4    Jiang, X.5    Wei, G.6
  • 8
    • 84899508795 scopus 로고    scopus 로고
    • Training set selection for the prediction of essential genes
    • Cheng, J., Xu, Z., Wu, W., Zhao, L., Li, X., Liu, Y., et al. (2014). Training set selection for the prediction of essential genes. PLoS ONE 9:e86805. doi: 10.1371/journal.pone.0086805
    • (2014) PLoS ONE , vol.9
    • Cheng, J.1    Xu, Z.2    Wu, W.3    Zhao, L.4    Li, X.5    Liu, Y.6
  • 9
    • 33947628597 scopus 로고    scopus 로고
    • Systems-level insights into cellular regulation: inferring, analysing, and modelling intracellular networks
    • Christensen, C., Thakar, J., and Albert, R. (2007). Systems-level insights into cellular regulation: inferring, analysing, and modelling intracellular networks. IET Syst Biol. 1, 61-77. doi: 10.1049/iet-syb:20060071
    • (2007) IET Syst Biol , vol.1 , pp. 61-77
    • Christensen, C.1    Thakar, J.2    Albert, R.3
  • 10
    • 26244440771 scopus 로고    scopus 로고
    • Gene essentiality and the topology of protein interaction networks
    • Coulomb, S., Bauer, M., Bernard, D., and Marsolier-Kergoat, M. C. (2005). Gene essentiality and the topology of protein interaction networks. Proc. Biol. Sci. 272, 1721-1725. doi: 10.1098/rspb.2005.3128
    • (2005) Proc. Biol. Sci , vol.272 , pp. 1721-1725
    • Coulomb, S.1    Bauer, M.2    Bernard, D.3    Marsolier-Kergoat, M.C.4
  • 11
    • 79951573994 scopus 로고    scopus 로고
    • Investigating the predictability of essential genes across distantly related organisms using an integrative approach
    • Deng, J., Deng, L., Su, S., Zhang, M., Lin, X., Wei, L., et al. (2011). Investigating the predictability of essential genes across distantly related organisms using an integrative approach. Nucleic Acids Res. 39, 795-807. doi: 10.1093/nar/gkq784
    • (2011) Nucleic Acids Res , vol.39 , pp. 795-807
    • Deng, J.1    Deng, L.2    Su, S.3    Zhang, M.4    Lin, X.5    Wei, L.6
  • 12
    • 26944450851 scopus 로고    scopus 로고
    • Subgraph centrality in complex networks
    • Estrada, E., and Rodríuez-Veláquez, J. A. (2005). Subgraph centrality in complex networks. Phys. Rev. E 71, 1-9. doi: 10.1103/PhysRevE.71.056103
    • (2005) Phys. Rev. E , vol.71 , pp. 1-9
    • Estrada, E.1    Rodríuez-Veláquez, J.A.2
  • 13
    • 33846504443 scopus 로고    scopus 로고
    • A comprehensive transposon mutant library of Francisella novicida, a bioweapon surrogate
    • Gallagher, L. A., Ramage, E., Jacobs, M. A., Kaul, R., Brittnacher, M., and Manoil, C. (2007). A comprehensive transposon mutant library of Francisella novicida, a bioweapon surrogate. Proc. Natl. Acad. Sci. U.S.A. 104, 1009-1014. doi: 10.1073/pnas.0606713104
    • (2007) Proc. Natl. Acad. Sci. U.S.A , vol.104 , pp. 1009-1014
    • Gallagher, L.A.1    Ramage, E.2    Jacobs, M.A.3    Kaul, R.4    Brittnacher, M.5    Manoil, C.6
  • 14
    • 0037173615 scopus 로고    scopus 로고
    • Functional profiling of the Saccharomyces cerevisiae genome
    • Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., et al. (2002). Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-391. doi: 10.1038/nature00935
    • (2002) Nature , vol.418 , pp. 387-391
    • Giaever, G.1    Chu, A.M.2    Ni, L.3    Connelly, C.4    Riles, L.5    Véronneau, S.6
  • 15
    • 33750488443 scopus 로고    scopus 로고
    • Towards the identification of essential genes using targeted genome sequencing and comparative analysis
    • Gustafson, A. M., Snitkin, E. S., Parker, S. C., DeLisi, C., and Kasif, S. (2006). Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics 7:265. doi: 10.1186/1471-2164-7-265
    • (2006) BMC Genomics , vol.7 , pp. 265
    • Gustafson, A.M.1    Snitkin, E.S.2    Parker, S.C.3    DeLisi, C.4    Kasif, S.5
  • 16
    • 0035694237 scopus 로고    scopus 로고
    • Identification of essential genes in cultured mammalian cells using small interfering RNAs
    • Harborth, J., Elbashir, S. M., Bechert, K., Tuschl, T., and Weber, K. (2001). Identification of essential genes in cultured mammalian cells using small interfering RNAs. J. Cell Sci. 114, 4557-4565.
    • (2001) J. Cell Sci , vol.114 , pp. 4557-4565
    • Harborth, J.1    Elbashir, S.M.2    Bechert, K.3    Tuschl, T.4    Weber, K.5
  • 17
    • 73849107815 scopus 로고    scopus 로고
    • Computational prediction of essential genes in an uncluturable endosymbiotic bacterium, Wolbachia of Brugia malayi
    • Holman, A. G., Davis, P. J., Foster, J. M., Carlow, C. K., and Sabjay, K. (2009). Computational prediction of essential genes in an uncluturable endosymbiotic bacterium, Wolbachia of Brugia malayi. BMC Microbiol. 9:243. doi: 10.1186/1471-2180-9-243
    • (2009) BMC Microbiol , vol.9 , pp. 243
    • Holman, A.G.1    Davis, P.J.2    Foster, J.M.3    Carlow, C.K.4    Sabjay, K.5
  • 18
    • 72949094885 scopus 로고    scopus 로고
    • Predicting essential genes based on network and sequence analysis
    • Hwang, Y. C., Lin, C. C., Chang, J. Y., Mori, H., Juan, H. F., and Huang, H. C. (2009). Predicting essential genes based on network and sequence analysis. Mol. Biosyst. 5, 1672-1678. doi: 10.1039/b900611g
    • (2009) Mol. Biosyst , vol.5 , pp. 1672-1678
    • Hwang, Y.C.1    Lin, C.C.2    Chang, J.Y.3    Mori, H.4    Juan, H.F.5    Huang, H.C.6
  • 19
    • 0036141992 scopus 로고    scopus 로고
    • Relating whole-genome expression data with protein-protein interactions
    • Jansen, R., Greenbaum, D., and Gerstein, M. (2002). Relating whole-genome expression data with protein-protein interactions. Genome Res. 12, 37-46. doi: 10.1101/gr.205602
    • (2002) Genome Res , vol.12 , pp. 37-46
    • Jansen, R.1    Greenbaum, D.2    Gerstein, M.3
  • 20
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong, H., Mason, S. P., Barabási, A. L., and Oltvai, Z. N. (2001). Lethality and centrality in protein networks. Nature 411, 41-42. doi: 10.1038/35075138
    • (2001) Nature , vol.411 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabási, A.L.3    Oltvai, Z.N.4
  • 21
    • 0035929121 scopus 로고    scopus 로고
    • Identification of critical staphylococcal genes using conditional phenotypes generated by antisense RNA
    • Ji, Y., Zhang, B., Van Horn, S. F., Warren, P., Woodnutt, G., Burnham, M. K., et al. (2001). Identification of critical staphylococcal genes using conditional phenotypes generated by antisense RNA. Science 293, 2266-2269. doi: 10.1126/science.1063566
    • (2001) Science , vol.293 , pp. 2266-2269
    • Ji, Y.1    Zhang, B.2    Van Horn, S.F.3    Warren, P.4    Woodnutt, G.5    Burnham, M.K.6
  • 22
    • 27744469130 scopus 로고    scopus 로고
    • High-betweenness proteins in the yeast protein interaction network
    • Joy, M. P., Brock, A., Ingber, D. E., and Huang, S. (2005). High-betweenness proteins in the yeast protein interaction network. J. Biomed. Biotechnol. 2, 96-103. doi: 10.1155/JBB.2005.96
    • (2005) J. Biomed. Biotechnol , vol.2 , pp. 96-103
    • Joy, M.P.1    Brock, A.2    Ingber, D.E.3    Huang, S.4
  • 23
    • 84863104679 scopus 로고    scopus 로고
    • High confidence prediction of essential genes in Burkholderia cenocepacia
    • Juhas, M., Stark, M., von Mering, C., Lumjiaktase, P., Crook, D. W., Valvano, M. A., et al. (2012). High confidence prediction of essential genes in Burkholderia cenocepacia. PLoS ONE 7:e40064. doi: 10.1371/journal.pone.0040064
    • (2012) PLoS ONE , vol.7
    • Juhas, M.1    Stark, M.2    von Mering, C.3    Lumjiaktase, P.4    Crook, D.W.5    Valvano, M.A.6
  • 24
    • 0037448540 scopus 로고    scopus 로고
    • Systematic functional analysis of the Caenorhabditis elegans genome using RNAi
    • Kamath, R. S., Fraser, A. G., Dong, Y., Poulin, G., Durbin, R., Gotta, M., et al. (2003). Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421, 231-237. doi: 10.1038/nature01278
    • (2003) Nature , vol.421 , pp. 231-237
    • Kamath, R.S.1    Fraser, A.G.2    Dong, Y.3    Poulin, G.4    Durbin, R.5    Gotta, M.6
  • 25
    • 51349111653 scopus 로고    scopus 로고
    • What are decision trees?
    • Kingsford, C., and Salzberg, S. L. (2008). What are decision trees? Nat. Biotechnol. 26, 1011-1013. doi: 10.1038/nbt0908-1011
    • (2008) Nat. Biotechnol , vol.26 , pp. 1011-1013
    • Kingsford, C.1    Salzberg, S.L.2
  • 26
    • 0038472048 scopus 로고    scopus 로고
    • A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: application to Mycobacterium tuberculosis
    • Lamichhane, G., Zignol, M., Blades, N. J., Geiman, D. E., Dougherty, A., Grosset, J., et al. (2003). A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: application to Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA. 100, 7213-7218. doi: 10.1073/pnas.1231432100
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 7213-7218
    • Lamichhane, G.1    Zignol, M.2    Blades, N.J.3    Geiman, D.E.4    Dougherty, A.5    Grosset, J.6
  • 27
    • 73249130761 scopus 로고    scopus 로고
    • Simultaneous assay of every Salmonella typhi gene using one million transposon mutants
    • Langridge, G. C., Phan, M. D., Turner, D. J., Perkins, T. T., Parts, L., Haase, J., et al. (2009). Simultaneous assay of every Salmonella typhi gene using one million transposon mutants. Genome Res. 19, 2308-2316. doi: 10.1101/gr.097097.109
    • (2009) Genome Res , vol.19 , pp. 2308-2316
    • Langridge, G.C.1    Phan, M.D.2    Turner, D.J.3    Perkins, T.T.4    Parts, L.5    Haase, J.6
  • 28
    • 0030342815 scopus 로고    scopus 로고
    • Combining estimates in regression and classification
    • Leblanc, M., and Tibshirane, R. (1996). Combining estimates in regression and classification. J. Am. Stat. Assoc. 91, 1641-1650. doi: 10.1080/01621459.1996.10476733
    • (1996) J. Am. Stat. Assoc , vol.91 , pp. 1641-1650
    • Leblanc, M.1    Tibshirane, R.2
  • 29
    • 84862787765 scopus 로고    scopus 로고
    • A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data
    • Li, M., Zhang, H., Wang, J., and Pan, Y. (2012). A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data. BMC Syst. Biol. 6:15. doi: 10.1186/1752-0509-6-15
    • (2012) BMC Syst. Biol , vol.6 , pp. 15
    • Li, M.1    Zhang, H.2    Wang, J.3    Pan, Y.4
  • 30
    • 84902296041 scopus 로고    scopus 로고
    • Predicting essential genes for identifying potential drug targets in Aspergillus fumigatus
    • Lu, Y., Deng, J., Rhodes, J. C., Lu, H., and Lu, L. J. (2014). Predicting essential genes for identifying potential drug targets in Aspergillus fumigatus. Comput. Biol. Chem. 50, 29-40. doi: 10.1016/j.compbiolchem.2014.01.011
    • (2014) Comput. Biol. Chem , vol.50 , pp. 29-40
    • Lu, Y.1    Deng, J.2    Rhodes, J.C.3    Lu, H.4    Lu, L.J.5
  • 31
    • 84964641354 scopus 로고    scopus 로고
    • 'Ten steps to mining your data'
    • ed. J. Mena (Newton, MA: Digital Press)
    • Mena, J. (1999). "Ten steps to mining your data" in Data Mining Your Website, ed J. Mena (Newton, MA: Digital Press), 136-145.
    • (1999) Data Mining Your Website , pp. 136-145
    • Mena, J.1
  • 33
    • 0029789824 scopus 로고    scopus 로고
    • A minimal gene set for cellular life derived by comparison of complete bacterial genomes
    • Mushegian, A. R., and Koonin, E. V. (1996). A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl. Acad. Sci. U.S.A. 93, 10268-10273. doi: 10.1073/pnas.93.19.10268
    • (1996) Proc. Natl. Acad. Sci. U.S.A , vol.93 , pp. 10268-10273
    • Mushegian, A.R.1    Koonin, E.V.2
  • 34
    • 78650475398 scopus 로고    scopus 로고
    • Phenotypic landscape of a bacterial cell
    • Nichols, R. J., Sen, S., Choo, Y. J., Beltrao, P., Zietek, M. Chaba, et al. (2011). Phenotypic landscape of a bacterial cell. Cell 144, 143-156. doi: 10.1016/j.cell.2010.11.052
    • (2011) Cell , vol.144 , pp. 143-156
    • Nichols, R.J.1    Sen, S.2    Choo, Y.J.3    Beltrao, P.4    Zietek, M.5    Chaba6
  • 35
    • 0000551189 scopus 로고    scopus 로고
    • Popular ensemble methods: an empirical study
    • Opitz, D., and Maclin, R. (1999). Popular ensemble methods: an empirical study. J. Artif. Intell. Res. 11, 169-198.
    • (1999) J. Artif. Intell. Res , vol.11 , pp. 169-198
    • Opitz, D.1    Maclin, R.2
  • 36
    • 77956031473 scopus 로고    scopus 로고
    • A survey on transfer learning
    • Pan, S. J., and Yang, Q. (2010). A survey on transfer learning. IEEE Trans. Knowl. Data Eng. 22, 1345-1359. doi: 10.1109/TKDE.2009.191
    • (2010) IEEE Trans. Knowl. Data Eng , vol.22 , pp. 1345-1359
    • Pan, S.J.1    Yang, Q.2
  • 37
    • 84867613437 scopus 로고    scopus 로고
    • Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks
    • Peng, W., Wang, J. X., Wang, W. P., Liu, Q., Wu, F. X., and Pan, Y. (2012). Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks. BMC Syst. Biol. 6:87. doi: 10.1186/1752-0509-6-87
    • (2012) BMC Syst. Biol , vol.6 , pp. 87
    • Peng, W.1    Wang, J.X.2    Wang, W.P.3    Liu, Q.4    Wu, F.X.5    Pan, Y.6
  • 38
    • 77955077532 scopus 로고    scopus 로고
    • Identifying essential genes in bacterial metabolic networks with machine learning methods
    • Plaimas, K., Eils, R., and König, R. (2010). Identifying essential genes in bacterial metabolic networks with machine learning methods. BMC Syst. Biol. 4:56. doi: 10.1186/1752-0509-4-56
    • (2010) BMC Syst. Biol , vol.4 , pp. 56
    • Plaimas, K.1    Eils, R.2    König, R.3
  • 39
    • 33748611921 scopus 로고    scopus 로고
    • Ensemble based systems in decision making
    • Polikar, R. (2006). Ensemble based systems in decision making. IEEE Circ. Syst. Mag. 6, 21-45. doi: 10.1109/MCAS.2006.1688199
    • (2006) IEEE Circ. Syst. Mag , vol.6 , pp. 21-45
    • Polikar, R.1
  • 40
    • 84904752421 scopus 로고    scopus 로고
    • Protein-protein interaction detection: methods and analysis
    • Rao, V. S., Srinivas, K., Sujini, G. N., and Kumar, G. N. (2014). Protein-protein interaction detection: methods and analysis. Int. J. Proteomics 2014, 147648. doi: 10.1155/2014/147648
    • (2014) Int. J. Proteomics , vol.2014
    • Rao, V.S.1    Srinivas, K.2    Sujini, G.N.3    Kumar, G.N.4
  • 41
    • 0141818929 scopus 로고    scopus 로고
    • Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery
    • Roemer, T., Jiang, B., Davison, J., Ketela, T., Veillette, K., Breton, A., et al. (2003). Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery. Mol. Microbiol. 50, 167-181. doi: 10.1046/j.1365-2958.2003.03697.x
    • (2003) Mol. Microbiol , vol.50 , pp. 167-181
    • Roemer, T.1    Jiang, B.2    Davison, J.3    Ketela, T.4    Veillette, K.5    Breton, A.6
  • 42
    • 84934877934 scopus 로고    scopus 로고
    • Analyzing complex networks through correlations in centrality measurements
    • Ronqui, J. R. F., and Travieso, G. (2015). Analyzing complex networks through correlations in centrality measurements. J. Stat. Mech. Theory E 2015, P05030. doi: 10.1088/1742-5468/2015/05/p05030
    • (2015) J. Stat. Mech. Theory E , vol.2015
    • Ronqui, J.R.F.1    Travieso, G.2
  • 43
    • 33749075731 scopus 로고    scopus 로고
    • In silico prediction of yeast deletion phenotypes
    • Saha, S., and Heber, S. (2006). In silico prediction of yeast deletion phenotypes. Genet. Mol. Res. 5, 224-232.
    • (2006) Genet. Mol. Res , vol.5 , pp. 224-232
    • Saha, S.1    Heber, S.2
  • 45
    • 36749009250 scopus 로고    scopus 로고
    • In silico network topology-based prediction of gene essentiality
    • Silva, J. P. M., Acencio, M. L., Mombach, J. C. M., Vieira, R., Silva, J. C., Siniaglia, M., et al. (2008). In silico network topology-based prediction of gene essentiality. Physica A 387, 1049-1055. doi: 10.1016/j.physa.2007.10.044
    • (2008) Physica A , vol.387 , pp. 1049-1055
    • Silva, J.P.M.1    Acencio, M.L.2    Mombach, J.C.M.3    Vieira, R.4    Silva, J.C.5    Siniaglia, M.6
  • 46
    • 84907885296 scopus 로고    scopus 로고
    • Nodes occupying central positions in human tissue specific PPI networks are enriched with many splice variants
    • Sinha, A., and Nagarajaram, H. A. (2014). Nodes occupying central positions in human tissue specific PPI networks are enriched with many splice variants. Proteomics 14, 2242-2248. doi: 10.1002/pmic.201400249
    • (2014) Proteomics , vol.14 , pp. 2242-2248
    • Sinha, A.1    Nagarajaram, H.A.2
  • 48
    • 45249126392 scopus 로고
    • Rethinking centrality: methods and examples
    • Stephenson, K., and Zelen, M. (1989). Rethinking centrality: methods and examples. Soc. Netw. 11, 1-37. doi: 10.1016/0378-8733(89)90016-6
    • (1989) Soc. Netw , vol.11 , pp. 1-37
    • Stephenson, K.1    Zelen, M.2
  • 49
    • 84872502627 scopus 로고    scopus 로고
    • 'Identifying essential proteins via integration of protein interaction and gene expression data, '
    • (Philadelphia, PA)
    • Tang, X., Wang, J. X., and Pan, Y. (2012). "Identifying essential proteins via integration of protein interaction and gene expression data, " in IEEE International Conference on Bioinformatics and Biomedicine (Philadelphia, PA), 1-4. doi: 10.1109/bibm.2012.6392716
    • (2012) IEEE International Conference on Bioinformatics and Biomedicine , pp. 1-4
    • Tang, X.1    Wang, J.X.2    Pan, Y.3
  • 50
    • 4143148491 scopus 로고    scopus 로고
    • Genome-scale identification of conditionally essential genes in E. coli by DNA microarrays
    • Tong, X., Campbell, J. W., Balázsi, G., Kay, K. A., Wanner, B. L., Gerdes, S. Y., et al. (2004). Genome-scale identification of conditionally essential genes in E. coli by DNA microarrays. Biochem. Biophys. Res. Commun. 322, 347-354. doi: 10.1016/j.bbrc.2004.07.110
    • (2004) Biochem. Biophys. Res. Commun , vol.322 , pp. 347-354
    • Tong, X.1    Campbell, J.W.2    Balázsi, G.3    Kay, K.A.4    Wanner, B.L.5    Gerdes, S.Y.6
  • 52
    • 84861492539 scopus 로고    scopus 로고
    • Identification of essential proteins based on edge clustering coefficient
    • Wang, J. X., Li, M., Wang, H., and Pan, Y. (2012). Identification of essential proteins based on edge clustering coefficient. IEEE/ACM Trans. Comput. Biol. Bioinform. 9, 1070-1080. doi: 10.1109/TCBB.2011.147
    • (2012) IEEE/ACM Trans. Comput. Biol. Bioinform , vol.9 , pp. 1070-1080
    • Wang, J.X.1    Li, M.2    Wang, H.3    Pan, Y.4
  • 53
    • 0033529707 scopus 로고    scopus 로고
    • Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis
    • Winzeler, E. A., Shoemaker, D. D., Astromoff, A., Liang, H., Anderson, K., Andre, B., et al. (1999). Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901-906. doi: 10.1126/science.285.5429.901
    • (1999) Science , vol.285 , pp. 901-906
    • Winzeler, E.A.1    Shoemaker, D.D.2    Astromoff, A.3    Liang, H.4    Anderson, K.5    Andre, B.6
  • 54
    • 0038700482 scopus 로고    scopus 로고
    • Centers of complex networks
    • Wuchty, S., and Stadler, P. F. (2003). Centers of complex networks. J. Theor. Biol. 223, 45-53. doi: 10.1016/S0022-5193(03)00071-7
    • (2003) J. Theor. Biol , vol.223 , pp. 45-53
    • Wuchty, S.1    Stadler, P.F.2
  • 55
    • 84887338297 scopus 로고    scopus 로고
    • CEG: a database of essential gene clusters
    • Ye, Y. N., Hua, Z. G., Huang, J., Rao, N., and Gao, F. B. (2013). CEG: a database of essential gene clusters. BMC Genomics 14:769. doi: 10.1186/1471-2164-14-769
    • (2013) BMC Genomics , vol.14 , pp. 769
    • Ye, Y.N.1    Hua, Z.G.2    Huang, J.3    Rao, N.4    Gao, F.B.5
  • 56
    • 34247622363 scopus 로고    scopus 로고
    • The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics
    • Yu, H., Kim, P. M., Sprecher, E., Trifonov, V., and Gerstein, M. (2007). The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput. Biol. 3:e59. doi: 10.1371/journal.pcbi.0030059
    • (2007) PLoS Comput. Biol , vol.3
    • Yu, H.1    Kim, P.M.2    Sprecher, E.3    Trifonov, V.4    Gerstein, M.5
  • 57
    • 58149197597 scopus 로고    scopus 로고
    • DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes
    • Zhang, R., and Lin, Y. (2009). DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res. 37, D455-D458. doi: 10.1093/nar/gkn858
    • (2009) Nucleic Acids Res , vol.37 , pp. D455-D458
    • Zhang, R.1    Lin, Y.2
  • 58
    • 84903872226 scopus 로고    scopus 로고
    • Prediction of essential proteins based on gene expression programming
    • Zhong, J. C., Wang, J. X., Peng, W., Zhang, Z., and Pan, Y. (2013). Prediction of essential proteins based on gene expression programming. BMC Genomics 14:S7. doi: 10.1186/1471-2164-14-S4-S7
    • (2013) BMC Genomics , vol.14 , pp. S7
    • Zhong, J.C.1    Wang, J.X.2    Peng, W.3    Zhang, Z.4    Pan, Y.5
  • 59
    • 50949092459 scopus 로고    scopus 로고
    • Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality
    • Zotenko, E., Mestre, J., O'Leary, D. P., and Przytycka, T. M. (2008). 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. 4:e1000140. doi: 10.1371/journal.pcbi.1000140
    • (2008) PLoS Comput. Biol , vol.4
    • Zotenko, E.1    Mestre, J.2    O'Leary, D.P.3    Przytycka, T.M.4


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