NDLI: Discovering Frequent Patterns of Functional Associations in Protein Interaction Networks for Function Prediction

Content Provider	IEEE Xplore Digital Library
Author	Young-Rae Cho Aidong Zhang
Copyright Year	2008
Description	Author affiliation: Dept. of Comput. Sci., State Univ. of New York, Buffalo, NY (Young-Rae Cho; Aidong Zhang)
Abstract	Predicting function from protein interaction networks has been challenging because of the intricate functional relationships among proteins. Most of the previous function prediction methods depend on the neighborhood of or the connected paths to known proteins, and remain low in accuracy. In this paper, we propose a novel approach for function prediction by detecting frequent patterns of functional associations in a protein interaction network. A set of functions that a protein performs is assigned into the corresponding node as a label. A functional association pattern is then represented as a labeled subgraph. Our FASPAM (frequent functional association pattern mining) algorithm efficiently finds the patterns that occur frequently in the network. It iteratively increases the size of frequent patterns by one node at a time by selective joining, and simplifies the network by a priori pruning. Using the yeast protein interaction network extracted from DIP, the FASPAM algorithm found more than 1,400 frequent patterns. By leave-one-out cross validation, our algorithm predicted functions from the frequent patterns with the accuracy of 86%, which is higher than the results from most previous methods.
Starting Page	59
Ending Page	65
File Size	248505
Page Count	7
File Format	PDF
ISBN	9780769534527
DOI	10.1109/BIBM.2008.21
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2008-11-03
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	protein interaction networks Prediction methods protein-protein interactions Proteins Computer science Fungi USA Councils Prediction algorithms Sampling methods Iterative algorithms function prediction Bioinformatics Electronics packaging
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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