NDLI: Effectively predicting protein functions by collective classification

Content Provider	IEEE Xplore Digital Library
Author	Wei Xiong Hui Liu Jihong Guan Shuigeng Zhou
Copyright Year	2012
Description	Author affiliation: School of Computer Science, and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China (Wei Xiong; Shuigeng Zhou) \|\| Research Lab of Information Management, Changzhou University, Jiangsu, China (Hui Liu) \|\| Department of Computer Science & Technology, Tongji University, Shanghai, China (Jihong Guan)
Abstract	The high-throughput technologies have led to vast amounts of protein-protein interaction (PPI) data, and a number of approaches based on PPI networks have been proposed for protein function prediction. However, these approaches do not work well if there is not enough PPI information. To address this issue, we propose a novel collective classification based approach that combines protein sequence information and PPI information to improve the prediction performance. We first reconstruct a PPI network by adding a number of computed edges based on protein sequence similarity, and then apply a collective classification algorithm to predict protein function based on the new PPI network. Experiments over two real datasets demonstrate that our approach outperforms most of existing approaches across a series of label situations, especially in sparsely-labeled networks where the existing approaches fail because of PPI information inadequacy. Experimental results also validate the robustness of our approach to the number of labeled proteins in PPI networks.
Starting Page	634
Ending Page	639
File Size	1475720
Page Count	6
File Format	PDF
ISBN	9781467327466
e-ISBN	9781467327473
e-ISBN	9781467327442
DOI	10.1109/BIBMW.2012.6470212
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-10-04
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Protein engineering Protein interaction network Protein function prediction Educational institutions Collective classification Mice Protein sequence Classification algorithms Bioinformatics Sequence similarity
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
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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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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