ISCB-Asia/SCCG 2012, session on cancer genome informatics


Shihua Zhang
Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing

Discovery of multi-dimensional modules by integrative analysis of cancer genomic data

Abstract

Recent technology has made it possible to simultaneously perform multi-platform genomic profiling (e.g., DNA methylation, and gene expression) of biological samples, resulting in so-called ``multi-dimensional genomic data". Such data provide unique opportunities to study the coordination between regulatory mechanisms on multiple levels. However, integrative analysis of multi-dimensional genomics data for the discovery of combinatorial patterns is currently lacking.

We adopt a joint matrix factorization technique to address this challenge. This method projects multiple types of genomic data onto a common coordinate system, in which heterogeneous variables weighted highly in the same projected direction form a multi-dimensional module. Genomic variables in such modules are characterized by significant correlations and likely functional associations. We applied this method to the DNA methylation, gene expression, and microRNA expression data of 385 ovarian cancer samples from the TCGA project. These multi-dimensional modules revealed perturbed pathways that would have been overlooked with only a single type of data, uncovered associations between different layers of cellular activities, and allowed the identification of clinically distinct patient subgroups. Our study provides an useful protocol for uncovering hidden patterns and their biological implications in multi-dimensional ``omic" data.

Biography

Shihua Zhang, Ph.D., was born in Shandong, China, in 1980. He received the B.S. degree and the Ph.D. degree from the Yunnan University and the Academy of Mathematics and Systems Science of CAS, in 2003 and 2008, respectively. Since 2008, Zhang has been an Assistant Professor of the Academy of Mathematics and Systems Science of CAS. From 2008 to 2010, he was a Visiting Postdoctoral Researcher at the University of Southern California, USA. He is mainly interested in computational problems in computational biology/bioinformatics/systems biology. In 2008, he was the recipient of the Special Presidential Prize of Chinese Academy of Science. In 2010, he was the recipient of the National Excellent Ph.D. Thesis Award in China.

His interests are within Bioinformatics, Computational Biology and Network Science, particularly in Cancer Genomics and Network Biology. He has published over 30 technical papers in the refereed journals and conference proceedings such as in Bioinformatics (including two ISMB papers), PLoS Computational Biology, Nucleic Acids Research, Proteomics, Plos ONE, BMC Systems Biology, BMC Bioinformatics, Physical Review E.