Daisuke Tominaga
National Institute of Advanced Industrial Science and Technology, Japan
Title: Multi-omics estimation on comprehensive measurement of gene expression levels to identify stress response pathways
Biography
Biography: Daisuke Tominaga
Abstract
Living cells respond to environmental stresses. Specific genes are expressed and pathways are activated in the responses. While changes in gene expression levels are today measured comprehensively with reasonable cost, measuring activities of each pathway is still difficult even many cutting-edge observation techniques such as one molecule observation methods have been realized. Therefore pathway activities are estimated from gene expression levels. By identifying the mechanisms of stress responses, introducing heat shock response mechanisms of some micro organisms to valuable and weak strain in heat, or using mouse as a model of human disease may be able.We tried to identify the activated pathway as the response to the stress from comprehensive gene expression level measurement by DNA microarrays. We measured sample in two conditions, under the stress and no stress, five sample in each, then the gene enrichment analysis was done on annotations of measured genes to calculated score values for each pathway appears in the annotation. First, we selected the median values of the five measurements as the expression values for each gene. Change values are calculated as logarithms of ratios of expression values of stressed samples to no stress samples for each gene. Top five percents of highly changing genes are selected as specifically changing genes. We calculated statistically p-values for each pathway that is annotated to all specifically changing genes by Fisher’s exact test. Then, pathways with low p-values are listed as those responding to the stress.