A protein sequence meta-functional signature for calcium binding residue prediction
Pattern Recognition Letters
Learning functional linkage networks with a cost-sensitive approach
Proceedings of the 2011 conference on Neural Nets WIRN10: Proceedings of the 20th Italian Workshop on Neural Nets
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Hi-index | 3.84 |
Motivation: Progress in large-scale experimental determination of protein--protein interaction networks for several organisms has resulted in innovative methods of functional inference based on network connectivity. However, the amount of effort and resources required for the elucidation of experimental protein interaction networks is prohibitive. Previously we, and others, have developed techniques to predict protein interactions for novel genomes using computational methods and data generated from other genomes. Results: We evaluated the performance of a network-based functional annotation method that makes use of our predicted protein interaction networks. We show that this approach performs equally well on experimentally derived and predicted interaction networks, for both manually and computationally assigned annotations. We applied the method to predicted protein interaction networks for over 50 organisms from all domains of life, providing annotations for many previously unannotated proteins and verifying existing low-confidence annotations. Availability: Functional predictions for over 50 organisms are available at http://bioverse.compbio.washington.edu and datasets used for analysis at http://data.compbio.washington.edu/misc/downloads/nannotation_data/ Contact: admin@bioverse.compbio.washington.edu Supplementary information: A supplemental appendix gives additional details not in the main text. (http://data.compbio.washington.edu/misc/downloads/nannotation_data/supplement.pdf).