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Title: Accurate and efficient gene function prediction using a multi-bacterial network
Abstract Motivation Nearly 40% of the genes in sequenced genomes have no experimentally or computationally derived functional annotations. To fill this gap, we seek to develop methods for network-based gene function prediction that can integrate heterogeneous data for multiple species with experimentally based functional annotations and systematically transfer them to newly sequenced organisms on a genome-wide scale. However, the large sizes of such networks pose a challenge for the scalability of current methods. Results We develop a label propagation algorithm called FastSinkSource. By formally bounding its rate of progress, we decrease the running time by a factor of 100 without sacrificing accuracy. We systematically evaluate many approaches to construct multi-species bacterial networks and apply FastSinkSource and other state-of-the-art methods to these networks. We find that the most accurate and efficient approach is to pre-compute annotation scores for species with experimental annotations, and then to transfer them to other organisms. In this manner, FastSinkSource runs in under 3 min for 200 bacterial species. Availability and implementation An implementation of our framework and all data used in this research are available at https://github.com/Murali-group/multi-species-GOA-prediction. Supplementary information Supplementary data are available at Bioinformatics online.  more » « less
Award ID(s):
1759858 1817736 1617678
PAR ID:
10279602
Author(s) / Creator(s):
; ;
Editor(s):
Lenore, Cowen
Date Published:
Journal Name:
Bioinformatics
Volume:
37
Issue:
6
ISSN:
1367-4803
Page Range / eLocation ID:
800 to 806
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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