Enabling More Sophisticated Gene Expression Analysis for Understanding Diseases and Optimizing Treatments

Participants: Difeng Dong, Donny Soh, Limsoon Wong

Background

We survey the progress in the analysis of gene expression data for the purposes of disease subtype diagnosis, new subtype discovery, and understanding of diseases and treatment responses. We find existing works fall short on several issues: these works provide little information on the interplay between selected genes; the collection of pathways that can be used, evaluated, and ranked against the observed expression data is limited; and a comprehensive set of rules for reasoning about relevant molecular events has not been compiled and formalized.

Objectives

We thus envision an advanced integrated framework, and are developing a system based on it, to provide biologically inspired solutions. It comprises:

Automated analysis and extraction of information from biomedical texts;
Targeted construction of known pathways; and
Direct hypothesis generation based on logical reasoning on, and tests for, consistencies and inconsistencies of observed data against known pathways.

Selected Publications

Guimei Liu, Jinyan Li, Kelvin Sin, Limsoon Wong. Distance-Based Subspace Clustering with Flexible Dimension Partitioning. Proceedings of 23rd IEEE International Conference on Data Engineering, pages 1250--1254, Istanbul, Turkey, April 2007 PDF, nClusters Software, V1.0
Donny Soh, Difeng Dong, Yike Guo, Limsoon Wong. Enabling More Sophisticated Gene Expression Analysis for Understanding Diseases and Optimizing Treatments. ACM SIGKDD Explorations, 9(1):3--14, June 2007. PDF
Wen-Son Hsieh, Ross Soo, Bee-Keow Peh, Thomas Loh, Difeng Dong, Donny Soh, Limsoon Wong, Simon Green, Judy Chiao, Chun-Ying Cui, Yoke-Fong Lai, Soo-Chin Lee, Benjamin Mow, Richie Soong, Manuel Salto-Tellez, Boon-Cher Goh. Pharmacodynamic Effects of Seliciclib, an Orally Administered Cell Cycle Modulator, in Undifferentiated Nasopharyngeal Cancer. Clinical Cancer Research, 15(4):1435--1442, February 2009. PDF
Difeng Dong, Chun-Ying Cui, Benjamin Mow, Limsoon Wong. Deciphering Drug Action and Escape Pathways: An Example on Nasopharyngeal Carcinoma. Proceedings of 1st International Conference on Bioinformatics and Computational Biology (BICOB2009), pages 199--210, New Orleans, USA, 8-10 April 2009. PDF, Drug Pathway Decipherer V1.0 (Nov 2007), Drug Pathway Decipherer V2.0 (Dec 2008)
Donny Soh, Difeng Dong, Yike Guo, Limsoon Wong. Consistency, Comprehensiveness, and Compatibility of Pathway Databases Manuscript, 23 September 2009. Supplementary Data
Donny Soh, Difeng Dong, Yike Guo, Limsoon Wong. Finding Consistent Disease Subnetwork Across Datasets. Manuscript, 23 September 2009. Supplementary Data
Guimei Liu, Kelvin Sim, Jinyan Li, Limsoon Wong. Efficient Mining of Distance-Based Subspace Clusters. Statistical Analysis and Data Mining, submitted. nClusters Software, V1.1

Selected Presentations

Limsoon Wong. Two Applications of Text Mining in Bioinformatics: Enhancing Protein Function Prediction and Enhancing Drug Pathway Inference. Invited talk at 7th Korea-Singapore Workshop on Bioinformatics & NLP, Seoul, Korea, 15 February 2008. PPT
Difeng Dong, Guimei Liu, Limsoon Wong. Drug Pathway Decipherer and Some Exciting Results in Protein Complex Prediction. Invited talk at Symposium on Biomolecular Mechanism Discovery with Computational Biology, Biopolis, Singapore, 14 August 2008. PPT
Limsoon Wong. Challenges in Understanding Pathways, Predicting Complexes, & Inferring Protein Function. Invited keynote at First International Workshop on Neuroinformatics, Bioinformatics, and Cognitive Science, South China University of Technology, Guangzhou, China, 4-6 June 2009. PPT
Limsoon Wong. Some of My Headaches in Gene Expression Analysis. Invited talk at Dept of Pediatrics, NUH, Singapore, 14 October 2009.

Acknowledgements

This project is supported in part by NUS ARF grant R-252-050-238-101/133 (Wong: 11/05 - 11/08) and an A*STAR AIP scholarship (Soh).

Last updated: 14/10/09, Limsoon Wong.