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Graph pyramids for protein function prediction

Cited 3 time in Web of Science Cited 3 time in Scopus
Authors
Sandhan, Tushar; Yoo, Youngjun; Choi, Jin Young; Kim, Sun
Issue Date
2015-05-29
Publisher
BioMed Central
Citation
BMC Medical Genomics, 8(Suppl 2):S12
Description
This is an Open Access article distributed under the terms of the Creative
Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly cited.
Abstract
Abstract

Background
Uncovering the hidden organizational characteristics and regularities among biological sequences is the key issue for detailed understanding of an underlying biological phenomenon. Thus pattern recognition from nucleic acid sequences is an important affair for protein function prediction. As proteins from the same family exhibit similar characteristics, homology based approaches predict protein functions via protein classification. But conventional classification approaches mostly rely on the global features by considering only strong protein similarity matches. This leads to significant loss of prediction accuracy.


Methods
Here we construct the Protein-Protein Similarity (PPS) network, which captures the subtle properties of protein families. The proposed method considers the local as well as the global features, by examining the interactions among 'weakly interacting proteins' in the PPS network and by using hierarchical graph analysis via the graph pyramid. Different underlying properties of the protein families are uncovered by operating the proposed graph based features at various pyramid levels.


Results
Experimental results on benchmark data sets show that the proposed hierarchical voting algorithm using graph pyramid helps to improve computational efficiency as well the protein classification accuracy. Quantitatively, among 14,086 test sequences, on an average the proposed method misclassified only 21.1 sequences whereas baseline BLAST score based global feature matching method misclassified 362.9 sequences. With each correctly classified test sequence, the fast incremental learning ability of the proposed method further enhances the training model. Thus it has achieved more than 96% protein classification accuracy using only 20% per class training data.
Language
English
URI
http://hdl.handle.net/10371/100678
DOI
https://doi.org/10.1186/1755-8794-8-S2-S12
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College of Engineering/Engineering Practice School (공과대학/대학원)Dept. of Computer Science and Engineering (컴퓨터공학부)Journal Papers (저널논문_컴퓨터공학부)
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