Abstract：
BACKGROUND:Genome-wide disease-gene finding approaches may sometimes provide us with a long list of candidate genes. Since using pure experimental approaches to verify all candidates could be expensive, a number of network-based methods have been developed to prioritize candidates. Such tools usually have a set of parameters pre-trained using available network data. This means that re-training network-based tools may be required when existing biological networks are updated or when networks from different sources are to be tried. RESULTS:We developed a parameter-free method, interconnectedness (ICN), to rank candidate genes by assessing the closeness of them to known disease genes in a network. ICN was tested using 1,993 known disease-gene associations and achieved a success rate of ~44% using a protein-protein interaction network under a test scenario of simulated linkage analysis. This performance is comparable with those of other well-known methods and ICN outperforms other methods when a candidate disease gene is not directly linked to known disease genes in a network. Interestingly, we show that a combined scoring strategy could enable ICN to achieve an even better performance (~50%) than other methods used alone. CONCLUSIONS:ICN, a user-friendly method, can well complement other network-based methods in the context of prioritizing candidate disease genes.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Hsu CL,Huang YH,Hsu CT,Yang UCdoi
10.1186/1471-2164-12-S3-S25subject
Has Abstractpub_date
2011-11-30 00:00:00pages
S25issn
1471-2164pii
1471-2164-12-S3-S25journal_volume
12 Suppl 3pub_type
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