Pathway-dependent effectiveness of network algorithms for gene prioritization

PLoS ONE

Volumn 10, Issue 6, 2015, Pages

  Shim, Jung Eun ^a   Hwang, Sohyun ^a   Lee, Insuk ^a  

^a Yonsei University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYESIAN LEARNING; BIOINFORMATICS; COMPUTER ANALYSIS; DIRECT NEIGHBORHOOD; GAUSSIAN SMOOTHING; GENE PRIORITIZATION; GENETIC ALGORITHM; HUMAN; INTERMETHOD COMPARISON; MACHINE LEARNING; NETWORK DIFFUSION; NETWORK LEARNING; NONHUMAN; PHENOTYPE; PREDICTION; RECEIVER OPERATING CHARACTERISTIC; WORM; ALGORITHM; ANIMAL; AREA UNDER THE CURVE; CAENORHABDITIS ELEGANS; GENE REGULATORY NETWORK;

ALGORITHMS; ANIMALS; AREA UNDER CURVE; CAENORHABDITIS ELEGANS; GENE REGULATORY NETWORKS; HUMANS; PHENOTYPE; ROC CURVE;

EID: 84939203504     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0130589     Document Type: Article

References (20)

1. Ideker T, Sharan R (2008) Protein networks in disease. Genome Res 18:644-652. doi: 10.1101/gr. 071852.107 PMID: 18381899
2. Lee I (2013) Network approaches to the genetic dissection of phenotypes in animals and humans. Anim Cells Syst 17:75-79.
3. Lehner B, Lee I (2008) Network-guided genetic screening: building, testing and using gene networks to predict gene function. Brief Funct Genomic Proteomic 7:217-227. doi: 10.1093/bfgp/eln020 PMID: 18445637
4. Lee I, Blom UM, Wang PI, Shim JE, Marcotte EM (2011) Prioritizing candidate disease genes by networkbased boosting of genome-wide association data. Genome Res 21:1109-1121. doi: 10.1101/gr. 118992.110 PMID: 21536720
5. Linghu B, Snitkin ES, Hu Z, Xia Y, Delisi C (2009) Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biol 10:R91. doi: 10.1186/gb-2009-10-9-r91 PMID: 19728866
6. Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, Kalyana-Sundaram S, et al. (2005) Probabilistic model of the human protein-protein interaction network. Nat Biotechnol 23:951-959. PMID: 16082366
7. Wu G, Feng X, Stein L (2010) A human functional protein interaction network and its application to cancer data analysis. Genome Biol 11:R53. doi: 10.1186/gb-2010-11-5-r53 PMID: 20482850
8. Wang PI, Marcotte EM (2010) It's the machine that matters: Predicting gene function and phenotype from protein networks. Journal of Proteomics 73:2277-2289. doi: 10.1016/j.jprot.2010.07.005 PMID: 20637909
9. Mostafavi S, Ray D, Warde-Farley D, Grouios C, Morris Q (2008) GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biology 9.
10. Berrar D, Flach P (2012) Caveats and pitfalls of ROC analysis in clinical microarray research (and how to avoid them). Brief Bioinform 13:83-97. doi: 10.1093/bib/bbr008 PMID: 21422066
11. Lee I, Lehner B, Vavouri T, Shin J, Fraser AG, Marcotte EM (2010) Predicting genetic modifier loci using functional gene networks. Genome Res 20:1143-1153. doi: 10.1101/gr.102749.109 PMID: 20538624
12. Yook K, Harris TW, Bieri T, Cabunoc A, Chan J, Chen WJ, et al. (2012) WormBase 2012: more genomes, more data, new website. Nucleic Acids Res 40:D735-741. doi: 10.1093/nar/gkr954 PMID: 22067452
13. Schriml LM, Arze C, Nadendla S, Chang YW, Mazaitis M, Felix V, et al. (2012) Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res 40:D940-946. doi: 10.1093/nar/gkr972 PMID: 22080554
14. Clark RD, Webster-Clark DJ (2008) Managing bias in ROC curves. J Comput Aided Mol Des 22:141-146. doi: 10.1007/s10822-008-9181-z PMID: 18256892
15. Sheridan RP, Singh SB, Fluder EM, Kearsley SK (2001) Protocols for bridging the peptide to nonpeptide gap in topological similarity searches. J Chem Inf Comput Sci 41:1395-1406. PMID: 11604041
16. Swamidass SJ, Azencott CA, Daily K, Baldi P (2010) A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval. Bioinformatics 26:1348-1356. doi: 10.1093/bioinformatics/btq140 PMID: 20378557
17. Truchon JF, Bayly CI (2007) Evaluating virtual screening methods: good and bad metrics for the "early recognition" problem. J Chem Inf Model 47:488-508. PMID: 17288412
18. Zhao W, Hevener KE, White SW, Lee RE, Boyett JM (2009) A statistical framework to evaluate virtual screening. BMC Bioinformatics 10:225. doi: 10.1186/1471-2105-10-225 PMID: 19619306
19. Linghu B, Snitkin ES, Hu ZJ, Xia Y, DeLisi C (2009) Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biology 10.
20. Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, et al. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 41:D808-815. doi: 10.1093/nar/gks1094 PMID: 23203871