메뉴 건너뛰기




Volumn 7, Issue , 2017, Pages

A large-scale benchmark of gene prioritization methods

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGY; GENE ONTOLOGY; GENE REGULATORY NETWORK; GENOME-WIDE ASSOCIATION STUDY; SOFTWARE;

EID: 85038827029     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep46598     Document Type: Article
Times cited : (41)

References (41)
  • 1
    • 79551643743 scopus 로고    scopus 로고
    • A guide to web tools to prioritize candidate genes
    • Tranchevent, L.-C. et al. A guide to web tools to prioritize candidate genes. Brief. Bioinform. 12, 22-32 (2011).
    • (2011) Brief. Bioinform. , vol.12 , pp. 22-32
    • Tranchevent, L.-C.1
  • 3
    • 84876917161 scopus 로고    scopus 로고
    • Chapter 15: Disease gene prioritization
    • Bromberg, Y. Chapter 15: disease gene prioritization. PLoS Comput. Biol. 9, e1002902 (2013).
    • (2013) PLoS Comput. Biol. , vol.9 , pp. e1002902
    • Bromberg, Y.1
  • 4
    • 79960904149 scopus 로고    scopus 로고
    • Web tools for the prioritization of candidate disease genes
    • Oti, M., Ballouz, S. & Wouters, M. A. Web tools for the prioritization of candidate disease genes. Methods Mol. Biol. 760, 189-206 (2011).
    • (2011) Methods Mol. Biol. , vol.760 , pp. 189-206
    • Oti, M.1    Ballouz, S.2    Wouters, M.A.3
  • 5
    • 84934441103 scopus 로고    scopus 로고
    • Computational approaches for human disease gene prediction and ranking
    • Zhu, C., Wu, C., Aronow, B. J. & Jegga, A. G. Computational approaches for human disease gene prediction and ranking. Adv. Exp. Med. Biol. 799, 69-84 (2014).
    • (2014) Adv. Exp. Med. Biol. , vol.799 , pp. 69-84
    • Zhu, C.1    Wu, C.2    Aronow, B.J.3    Jegga, A.G.4
  • 6
    • 13444266370 scopus 로고    scopus 로고
    • Online mendelian inheritance in man (OMIM), a knowledgebase of human genes and genetic disorders
    • Hamosh, A., and Scott, A. F., Amberger, J. S., Bocchini, C. A. & McKusick, V. A. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 33, D514-7 (2005).
    • (2005) Nucleic Acids Res. , vol.33 , pp. D514-D517
    • Hamosh, A.1    Scott, A.F.2    Amberger, J.S.3    Bocchini, C.A.4    McKusick, V.A.5
  • 7
    • 84870474023 scopus 로고    scopus 로고
    • An unbiased evaluation of gene prioritization tools
    • Börnigen, D. et al. An unbiased evaluation of gene prioritization tools. Bioinformatics 28, 3081-8 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 3081-3088
    • Börnigen, D.1
  • 8
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • The Gene Ontology Consortium
    • Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-9 (2000).
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 9
    • 84891781481 scopus 로고    scopus 로고
    • FunCoup 3.0: Database of genome-wide functional coupling networks
    • Schmitt, T., Ogris, C. & Sonnhammer, E. L. L. FunCoup 3.0: database of genome-wide functional coupling networks. Nucleic Acids Res. 42, D380-8 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. D380-D388
    • Schmitt, T.1    Ogris, C.2    Sonnhammer, E.L.L.3
  • 10
    • 84862185886 scopus 로고    scopus 로고
    • Comparative interactomics with funcoup 2.0
    • Alexeyenko, A. et al. Comparative interactomics with Funcoup 2.0. Nucleic Acids Res. 40, 821-828 (2011).
    • (2011) Nucleic Acids Res. , vol.40 , pp. 821-828
    • Alexeyenko, A.1
  • 11
    • 65349085291 scopus 로고    scopus 로고
    • Global networks of functional coupling in Eukaryotes from comprehensive data integration
    • Alexeyenko, A. & Sonnhammer, E. L. L. Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res. 19, 1107-16 (2009).
    • (2009) Genome Res. , vol.19 , pp. 1107-1116
    • Alexeyenko, A.1    Sonnhammer, E.L.L.2
  • 12
    • 47549116997 scopus 로고    scopus 로고
    • A critical assessment of mus musculus gene function prediction using integrated genomic evidence
    • Peña-castillo, L. et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome⋯ 9, 1-19 (2008).
    • (2008) Genome⋯ , vol.9 , pp. 1-19
    • Peña-Castillo, L.1
  • 13
    • 85164392958 scopus 로고    scopus 로고
    • A study of cross-validation and bootstrap for accuracy estimation and model selection
    • (Morgan Kauffmann Publishers Inc., 1995)
    • Kohavi, R. A study of cross-validation and bootstrap for accuracy estimation and model selection. in IJCAI'95 Proc. 14th Int. Jt. Conf. Artif. Intell. - Vol. 2, 1137-1143 at http://dl.acm.org/citation.cfm?id=1643031.1643047 (Morgan Kauffmann Publishers Inc., 1995).
    • IJCAI'95 Proc. 14th Int. Jt. Conf. Artif. Intell , vol.2 , pp. 1137-1143
    • Kohavi, R.1
  • 14
    • 84951294736 scopus 로고    scopus 로고
    • November (2014)
    • Waskom, M. et al. seaborn: v0.5.0 (November 2014), doi: 10.5281/zenodo.12710 (2014).
    • (2014) Seaborn: V0.5.0
    • Waskom, M.1
  • 15
    • 0031191630 scopus 로고    scopus 로고
    • The use of the area under the roc curve in the evaluation of machine learning algorithms
    • Bradley, A. P. et al. The use of the area under the roc curve in the evaluation of machine learning algorithms. Pattern Recognit. 30, 1145-1159 (1997).
    • (1997) Pattern Recognit. , vol.30 , pp. 1145-1159
    • Bradley, A.P.1
  • 16
    • 1842637192 scopus 로고    scopus 로고
    • Cumulated gain-based evaluation of {IR} techniques
    • Järvelin, K. & Kekäläinen, J. Cumulated Gain-based Evaluation of {IR} Techniques. ACM Trans. Inf. Syst. 20, 422-446 (2002).
    • (2002) ACM Trans. Inf. Syst. , vol.20 , pp. 422-446
    • Järvelin, K.1    Kekäläinen, J.2
  • 17
    • 0002322469 scopus 로고
    • On a test of whether one of two random variables is stochastically larger than the other
    • Mann, H. B. & Whitney, D. R. On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other. Ann. Math. Stat. 18, 50-60 (1947).
    • (1947) Ann. Math. Stat. , vol.18 , pp. 50-60
    • Mann, H.B.1    Whitney, D.R.2
  • 18
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. & Hochberg, Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J. R. Stat. Soc. Ser. B 57, 289-300 (1995).
    • (1995) J. R. Stat. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 19
    • 84855731050 scopus 로고    scopus 로고
    • Ensembl BioMarts: A hub for data retrieval across taxonomic space
    • Kinsella, R. J. et al. Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford). 2011, bar030 (2011).
    • (2011) Database (Oxford). , vol.2011 , pp. bar030
    • Kinsella, R.J.1
  • 20
    • 84863987708 scopus 로고    scopus 로고
    • Computational tools for prioritizing candidate genes: Boosting disease gene discovery
    • Moreau, Y. & Tranchevent, L.-C. Computational tools for prioritizing candidate genes: boosting disease gene discovery. Nat. Rev. Genet. 13, 523-36 (2012).
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 523-536
    • Moreau, Y.1    Tranchevent, L.-C.2
  • 21
    • 84941051170 scopus 로고    scopus 로고
    • STRING v10: Protein-protein interaction networks, integrated over the tree of life
    • Szklarczyk, D. et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43, D447-52 (2015).
    • (2015) Nucleic Acids Res. , vol.43 , pp. D447-D452
    • Szklarczyk, D.1
  • 22
    • 84907485965 scopus 로고    scopus 로고
    • MaxLink: Network-based prioritization of genes tightly linked to a disease seed set
    • Guala, D., Sjölund, E. & Sonnhammer, E. L. L. MaxLink: network-based prioritization of genes tightly linked to a disease seed set. Bioinformatics 30, 2689-90 (2014).
    • (2014) Bioinformatics , vol.30 , pp. 2689-2690
    • Guala, D.1    Sjölund, E.2    Sonnhammer, E.L.L.3
  • 24
    • 79959898376 scopus 로고    scopus 로고
    • Prioritizing candidate disease genes by network-based boosting of genome-wide association data
    • Lee, I., and Blom, U. M., Wang, P. I., Shim, J. E. & Marcotte, E. M. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res. 21, 1109-21 (2011).
    • (2011) Genome Res. , vol.21 , pp. 1109-1121
    • Lee, I.1    Blom, U.M.2    Wang, P.I.3    Shim, J.E.4    Marcotte, E.M.5
  • 25
    • 84866683906 scopus 로고    scopus 로고
    • Exploiting protein-protein interaction networks for genome-wide disease-gene prioritization
    • Guney, E. & Oliva, B. Exploiting protein-protein interaction networks for genome-wide disease-gene prioritization. PLoS One 7, e43557 (2012).
    • (2012) PLoS One , vol.7 , pp. e43557
    • Guney, E.1    Oliva, B.2
  • 27
    • 62849126285 scopus 로고    scopus 로고
    • Disease candidate gene identification and prioritization using protein interaction networks
    • Chen, J., Aronow, B. J. & Jegga, A. G. Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinformatics 10, 73 (2009).
    • (2009) BMC Bioinformatics , vol.10 , pp. 73
    • Chen, J.1    Aronow, B.J.2    Jegga, A.G.3
  • 28
    • 41549139527 scopus 로고    scopus 로고
    • Walking the interactome for prioritization of candidate disease genes
    • Köhler, S., Bauer, S., Horn, D. & Robinson, P. N. Walking the interactome for prioritization of candidate disease genes. Am. J. Hum. Genet. 82, 949-58 (2008).
    • (2008) Am. J. Hum. Genet. , vol.82 , pp. 949-958
    • Köhler, S.1    Bauer, S.2    Horn, D.3    Robinson, P.N.4
  • 29
    • 84874736224 scopus 로고    scopus 로고
    • Neighbor-favoring weight reinforcement to improve random walk-based disease gene prioritization
    • Le, D.-H. & Kwon, Y.-K. Neighbor-favoring weight reinforcement to improve random walk-based disease gene prioritization. Comput. Biol. Chem. 44, 1-8 (2013).
    • (2013) Comput. Biol. Chem. , vol.44 , pp. 1-8
    • Le, D.-H.1    Kwon, Y.-K.2
  • 30
    • 84865053376 scopus 로고    scopus 로고
    • RESQUE: Network reduction using semi-Markov random walk scores for eficient querying of biological networks
    • Ebrahim Sahraeian, S. M. & Yoon, B.-J. RESQUE: Network Reduction Using Semi-Markov Random Walk Scores for Eficient Querying of Biological Networks. Bioinformatics 28, 2129-2136 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 2129-2136
    • Ebrahim Sahraeian, S.M.1    Yoon, B.-J.2
  • 32
    • 84878789737 scopus 로고    scopus 로고
    • Disease gene identification by random walk on multigraphs merging heterogeneous genomic and phenotype data
    • Li, Y. & Li, J. Disease gene identification by random walk on multigraphs merging heterogeneous genomic and phenotype data. BMC Genomics 13 Suppl 7 (2012).
    • (2012) BMC Genomics , vol.13
    • Li, Y.1    Li, J.2
  • 33
    • 84928651569 scopus 로고    scopus 로고
    • Network-based phenome-genome association prediction by Bi-Random walk
    • Xie, M., Xu, Y., Zhang, Y., Hwang, T. & Kuang, R. Network-based Phenome-Genome Association Prediction by Bi-Random Walk. PLoS One 10, e0125138 (2015).
    • (2015) PLoS One , vol.10 , pp. e0125138
    • Xie, M.1    Xu, Y.2    Zhang, Y.3    Hwang, T.4    Kuang, R.5
  • 34
    • 76749134818 scopus 로고    scopus 로고
    • Associating genes and protein complexes with disease via network propagation
    • Vanunu, O., Magger, O., Ruppin, E., Shlomi, T. & Sharan, R. Associating genes and protein complexes with disease via network propagation. PLoS Comput. Biol. 6, e1000641 (2010).
    • (2010) PLoS Comput. Biol. , vol.6 , pp. e1000641
    • Vanunu, O.1    Magger, O.2    Ruppin, E.3    Shlomi, T.4    Sharan, R.5
  • 35
    • 84862249788 scopus 로고    scopus 로고
    • Prioritizing disease candidate genes by a gene interconnectedness-based approach
    • Hsu, C.-L., Huang, Y.-H., Hsu, C.-T. & Yang, U.-C. Prioritizing disease candidate genes by a gene interconnectedness-based approach. BMC Genomics 12 Suppl 3, S25 (2011).
    • (2011) BMC Genomics , vol.12 , pp. S25
    • Hsu, C.-L.1    Huang, Y.-H.2    Hsu, C.-T.3    Yang, U.-C.4
  • 36
    • 85029604507 scopus 로고    scopus 로고
    • Inferring microRNA-disease associations by random walk on a heterogeneous network with multiple data sources
    • Liu, Y., Zeng, X., He, Z. & Zou, Q. Inferring microRNA-disease associations by random walk on a heterogeneous network with multiple data sources. IEEE/ACM Trans. Comput. Biol. Bioinforma. 1-1, doi: 10.1109/TCBB.2016.2550432 (2016).
    • (2016) IEEE/ACM Trans. Comput. Biol. Bioinforma , pp. 1
    • Liu, Y.1    Zeng, X.2    He, Z.3    Zou, Q.4
  • 38
    • 84939203504 scopus 로고    scopus 로고
    • Pathway-dependent effectiveness of network algorithms for gene prioritization
    • Shim, J. E., Hwang, S. & Lee, I. Pathway-Dependent Effectiveness of Network Algorithms for Gene Prioritization. PLoS One 10, e0130589 (2015).
    • (2015) PLoS One , vol.10 , pp. e0130589
    • Shim, J.E.1    Hwang, S.2    Lee, I.3
  • 39
    • 84926666370 scopus 로고    scopus 로고
    • Disease gene prioritization using network and feature
    • Xie, B. et al. Disease gene prioritization using network and feature. J. Comput. Biol. 22, 313-23 (2015).
    • (2015) J. Comput. Biol. , vol.22 , pp. 313-323
    • Xie, B.1
  • 40
    • 48449097800 scopus 로고    scopus 로고
    • ENDEAVOUR update: A web resource for gene prioritization in multiple species
    • Tranchevent, L.-C. et al. ENDEAVOUR update: a web resource for gene prioritization in multiple species. Nucleic Acids Res. 36, W377-84 (2008).
    • (2008) Nucleic Acids Res. , vol.36 , pp. W377-W384
    • Tranchevent, L.-C.1
  • 41
    • 79959922954 scopus 로고    scopus 로고
    • PINTA: A web server for network-based gene prioritization from expression data
    • Nitsch, D. et al. PINTA: a web server for network-based gene prioritization from expression data. Nucleic Acids Res. 39, W334-8 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. W334-W338
    • Nitsch, D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.