Abstract:
BACKGROUND:Although most of the current disease candidate gene identification and prioritization methods depend on functional annotations, the coverage of the gene functional annotations is a limiting factor. In the current study, we describe a candidate gene prioritization method that is entirely based on protein-protein interaction network (PPIN) analyses. RESULTS:For the first time, extended versions of the PageRank and HITS algorithms, and the K-Step Markov method are applied to prioritize disease candidate genes in a training-test schema. Using a list of known disease-related genes from our earlier study as a training set ("seeds"), and the rest of the known genes as a test list, we perform large-scale cross validation to rank the candidate genes and also evaluate and compare the performance of our approach. Under appropriate settings - for example, a back probability of 0.3 for PageRank with Priors and HITS with Priors, and step size 6 for K-Step Markov method - the three methods achieved a comparable AUC value, suggesting a similar performance. CONCLUSION:Even though network-based methods are generally not as effective as integrated functional annotation-based methods for disease candidate gene prioritization, in a one-to-one comparison, PPIN-based candidate gene prioritization performs better than all other gene features or annotations. Additionally, we demonstrate that methods used for studying both social and Web networks can be successfully used for disease candidate gene prioritization.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Chen J,Aronow BJ,Jegga AGdoi
10.1186/1471-2105-10-73subject
Has Abstractpub_date
2009-02-27 00:00:00pages
73issn
1471-2105pii
1471-2105-10-73journal_volume
10pub_type
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