Prioritizing disease genes by bi-random walk

Maoqiang Xie; Taehyun Hwang; Rui Kuang

doi:10.1007/978-3-642-30220-6_25

Prioritizing disease genes by bi-random walk

Maoqiang Xie, Taehyun Hwang, Rui Kuang

Computer Science and Engineering

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

43 Scopus citations

Abstract

Random walk methods have been successfully applied to prioritizing disease causal genes. In this paper, we propose a bi-random walk algorithm (BiRW) based on a regularization framework for graph matching to globally prioritize disease genes for all phenotypes simultaneously. While previous methods perform random walk either on the protein-protein interaction network or the complete phenome-genome heterogenous network, BiRW performs random walk on the Kronecker product graph between the protein-protein interaction network and the phenotype similarity network. Three variations of BiRW that perform balanced or unbalanced bi-directional random walks are analyzed and compared with other random walk methods. Experiments on analyzing the disease phenotype-gene associations in Online Mendelian Inheritance in Man (OMIM) demonstrate that BiRW effectively improved disease gene prioritization over existing methods by ranking more known associations in the top 100 out of nearly 10,000 candidate genes.

Original language	English (US)
Title of host publication	Advances in Knowledge Discovery and Data Mining - 16th Pacific-Asia Conference, PAKDD 2012, Proceedings
Pages	292-303
Number of pages	12
Edition	PART 2
DOIs	https://doi.org/10.1007/978-3-642-30220-6_25
State	Published - May 29 2012
Event	16th Pacific-Asia Conference on Advances in Knowledge Discovery and Data Mining, PAKDD 2012 - Kuala Lumpur, Malaysia Duration: May 29 2012 → Jun 1 2012

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Number	PART 2
Volume	7301 LNAI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	16th Pacific-Asia Conference on Advances in Knowledge Discovery and Data Mining, PAKDD 2012
Country/Territory	Malaysia
City	Kuala Lumpur
Period	5/29/12 → 6/1/12

Keywords

Bi-Random Walk
Disease Gene Prioritization
Graph-based Learning

Publisher link

10.1007/978-3-642-30220-6_25

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Xie, M., Hwang, T., & Kuang, R. (2012). Prioritizing disease genes by bi-random walk. In Advances in Knowledge Discovery and Data Mining - 16th Pacific-Asia Conference, PAKDD 2012, Proceedings (PART 2 ed., pp. 292-303). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7301 LNAI, No. PART 2). https://doi.org/10.1007/978-3-642-30220-6_25

Prioritizing disease genes by bi-random walk. / Xie, Maoqiang; Hwang, Taehyun; Kuang, Rui.
Advances in Knowledge Discovery and Data Mining - 16th Pacific-Asia Conference, PAKDD 2012, Proceedings. PART 2. ed. 2012. p. 292-303 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7301 LNAI, No. PART 2).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Xie, M, Hwang, T & Kuang, R 2012, Prioritizing disease genes by bi-random walk. in Advances in Knowledge Discovery and Data Mining - 16th Pacific-Asia Conference, PAKDD 2012, Proceedings. PART 2 edn, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), no. PART 2, vol. 7301 LNAI, pp. 292-303, 16th Pacific-Asia Conference on Advances in Knowledge Discovery and Data Mining, PAKDD 2012, Kuala Lumpur, Malaysia, 5/29/12. https://doi.org/10.1007/978-3-642-30220-6_25

Xie M, Hwang T, Kuang R. Prioritizing disease genes by bi-random walk. In Advances in Knowledge Discovery and Data Mining - 16th Pacific-Asia Conference, PAKDD 2012, Proceedings. PART 2 ed. 2012. p. 292-303. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); PART 2). doi: 10.1007/978-3-642-30220-6_25

Xie, Maoqiang ; Hwang, Taehyun ; Kuang, Rui. / Prioritizing disease genes by bi-random walk. Advances in Knowledge Discovery and Data Mining - 16th Pacific-Asia Conference, PAKDD 2012, Proceedings. PART 2. ed. 2012. pp. 292-303 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); PART 2).

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Prioritizing disease genes by bi-random walk

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