Prioritizing disease genes by bi-random walk

Maoqiang Xie, Taehyun Hwang, Rui Kuang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

23 Citations (Scopus)

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 languageEnglish (US)
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages292-303
Number of pages12
Volume7301 LNAI
EditionPART 2
DOIs
StatePublished - 2012
Event16th Pacific-Asia Conference on Advances in Knowledge Discovery and Data Mining, PAKDD 2012 - Kuala Lumpur, Malaysia
Duration: May 29 2012Jun 1 2012

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
NumberPART 2
Volume7301 LNAI
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other16th Pacific-Asia Conference on Advances in Knowledge Discovery and Data Mining, PAKDD 2012
CountryMalaysia
CityKuala Lumpur
Period5/29/126/1/12

Fingerprint

Random walk
Genes
Gene
Proteins
Phenotype
Protein Interaction Networks
Protein-protein Interaction
Product Graph
Graph Matching
Kronecker Product
Prioritization
Regularization
Ranking
Genome
Experiments
Demonstrate
Experiment

Keywords

  • Bi-Random Walk
  • Disease Gene Prioritization
  • Graph-based Learning

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

Cite this

Xie, M., Hwang, T., & Kuang, R. (2012). Prioritizing disease genes by bi-random walk. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (PART 2 ed., Vol. 7301 LNAI, 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.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 7301 LNAI 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 proceedingConference contribution

Xie, M, Hwang, T & Kuang, R 2012, Prioritizing disease genes by bi-random walk. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PART 2 edn, vol. 7301 LNAI, 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 Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PART 2 ed. Vol. 7301 LNAI. 2012. p. 292-303. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); PART 2). https://doi.org/10.1007/978-3-642-30220-6_25
Xie, Maoqiang ; Hwang, Taehyun ; Kuang, Rui. / Prioritizing disease genes by bi-random walk. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 7301 LNAI 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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