NDLI: Integrating Genomic Data and Topological Metrics to Obtain Reliable Protein-Protein Interactions

Content Provider	IEEE Xplore Digital Library
Author	Yang Xiao-fei Zheng Hao-ran Han Si-yuan Zhang Kuan
Copyright Year	2009
Abstract	Recent high-throughput (HTP) technology has accumulated a large amount of protein-protein interaction (PPI) data. However, these data are laden with high false positive and false negative rate. Here we combine genomic data and topological metrics to eliminate false positive high-throughput PPIs, and utilize other genomic information that is not integrated in the previous stage to justify the outcome. We devise an approach to remove highly probable false positive HTP PPIs from HTP dataset. Our method takes the advantage of two acknowledged facts about PPI: (1) Two interacting proteins often show similar or related genomic features, for instance, similar gene expression profile; (2) The protein interaction network is believed to possess some certain topological properties. First, we calculate a confidence value for each HTP PPI according to gene co-expression, co-essentiality and times observed in different HTP experiments. Then, topological metrics is used to give a topological weight to an interaction. The two weights are summed up to represent initial weight of interactions in raw PPI network. Next, we use IRAP procedure to iteratively remove false positives. To demonstrate the usefulness of our approach, Gene Ontology-biological process annotation information is utilized to evaluate the ultimate refined PPIs.
Starting Page	57
Ending Page	60
File Size	559447
Page Count	4
File Format	PDF
ISBN	9780769537351
DOI	10.1109/FSKD.2009.250
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2009-08-14
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Maximum likelihood estimation Protein engineering protein protein interaction Genomics Ontologies Throughput Gene expression high throughput Computer science gene ontology genomic Biological processes Bioinformatics Fuzzy systems topological metric
Content Type	Text
Resource Type	Article

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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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