Gene clustering is a method for finding gene sets which are related to the same biological processes or molecular function. In order to find these gene sets, previous studies have clustered genes which showed similar mRNA expression or a specific expression pattern in a (sub) sample set. However, for two contrasting groups of samples, it is not easy to identify gene sets which show significant expression pattern in only one group using current gene clustering methods. Existing biclustering methods use only one group (disease) of samples. It is hard to identify disease specific biclusters which are differentially expressed in the disease although those methods can find biclusters which have specific expression pattern. Here, we proposed a novel method using a genetic algorithm in gene expression data, in order to find gene sets which can represent specific subtype of cancer. Proposed method finds gene sets which have statistically differential mRNA expression on two contrasting samples and fraction of cancer samples. The resulting gene modules share higher number of GO (Gene Ontology) terms related to a specific disease than gene modules identified by current algorithms. We also identify that when we integrate protein-protein interaction data with gene expression data of colorectal cancer samples, proposed method can find more functionally related gene sets.
|Title of host publication||Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014|
|Editors||Huiru Zheng, Xiaohua Tony Hu, Daniel Berrar, Yadong Wang, Werner Dubitzky, Jin-Kao Hao, Kwang-Hyun Cho, David Gilbert|
|Publisher||Institute of Electrical and Electronics Engineers Inc.|
|Number of pages||4|
|Publication status||Published - 2014 Dec 29|
|Event||2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014 - Belfast, United Kingdom|
Duration: 2014 Nov 2 → 2014 Nov 5
|Name||Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014|
|Other||2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014|
|Period||14/11/2 → 14/11/5|
Bibliographical notePublisher Copyright:
© 2014 IEEE.
All Science Journal Classification (ASJC) codes
- Biomedical Engineering
- Health Informatics