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Techniques for transferring host-pathogen protein interactions knowledge to new tasks
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Kshirsagar, Meghana, Schleker, Sylvia, Carbonell, Jaime and Klein-Seetharaman, Judith (2015) Techniques for transferring host-pathogen protein interactions knowledge to new tasks. Frontiers in Microbiology, 6 . 36. doi:10.3389/fmicb.2015.00036 ISSN 1664-302X.
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Official URL: http://dx.doi.org/10.3389/fmicb.2015.00036
Abstract
We consider the problem of building a model to predict protein-protein interactions (PPIs) between the bacterial species Salmonella Typhimurium and the plant host Arabidopsis thaliana which is a host-pathogen pair for which no known PPIs are available. To achieve this, we present approaches, which use homology and statistical learning methods called “transfer learning.” In the transfer learning setting, the task of predicting PPIs between Arabidopsis and its pathogen S. Typhimurium is called the “target task.” The presented approaches utilize labeled data i.e., known PPIs of other host-pathogen pairs (we call these PPIs the “source tasks”). The homology based approaches use heuristics based on biological intuition to predict PPIs. The transfer learning methods use the similarity of the PPIs from the source tasks to the target task to build a model. For a quantitative evaluation we consider Salmonella-mouse PPI prediction and some other host-pathogen tasks where known PPIs exist. We use metrics such as precision and recall and our results show that our methods perform well on the target task in various transfer settings. We present a brief qualitative analysis of the Arabidopsis-Salmonella predicted interactions. We filter the predictions from all approaches using Gene Ontology term enrichment and only those interactions involving Salmonella effectors. Thereby we observe that Arabidopsis proteins involved e.g., in transcriptional regulation, hormone mediated signaling and defense response may be affected by Salmonella.
Item Type: | Journal Article | ||||||||
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Subjects: | Q Science > QR Microbiology | ||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Translational & Experimental Medicine > Metabolic and Vascular Health (- until July 2016) Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Translational & Experimental Medicine Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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Library of Congress Subject Headings (LCSH): | Salmonella typhimurium, Arabidopsis thaliana, Protein-protein interactions -- Mathematical models | ||||||||
Journal or Publication Title: | Frontiers in Microbiology | ||||||||
Publisher: | Frontiers Research Foundation | ||||||||
ISSN: | 1664-302X | ||||||||
Official Date: | 2 February 2015 | ||||||||
Dates: |
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Volume: | 6 | ||||||||
Article Number: | 36 | ||||||||
DOI: | 10.3389/fmicb.2015.00036 | ||||||||
Status: | Peer Reviewed | ||||||||
Publication Status: | Published | ||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||
Date of first compliant deposit: | 31 January 2017 | ||||||||
Date of first compliant Open Access: | 31 January 2017 |
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