title: Tracking difference in gene expression in a time-course experiment using gene set enrichment analysis.
abstract: Fistulifera sp. strain JPCC DA0580 is a newly sequenced pennate diatom that is capable of simultaneously growing and accumulating lipids. This is a unique trait, not found in other related microalgae so far. It is able to accumulate between 40 to 60% of its cell weight in lipids, making it a strong candidate for the production of biofuel. To investigate this characteristic, we used RNA-Seq data gathered at four different times while Fistulifera sp. strain JPCC DA0580 was grown in oil accumulating and non-oil accumulating conditions. We then adapted gene set enrichment analysis (GSEA) to investigate the relationship between the difference in gene expression of 7,822 genes and metabolic functions in our data. We utilized information in the KEGG pathway database to create the gene sets and changed GSEA to use re-sampling so that data from the different time points could be included in the analysis. Our GSEA method identified photosynthesis, lipid synthesis and amino acid synthesis related pathways as processes that play a significant role in oil production and growth in Fistulifera sp. strain JPCC DA0580. In addition to GSEA, we visualized the results by creating a network of compounds and reactions, and plotted the expression data on top of the network. This made existing graph algorithms available to us which we then used to calculate a path that metabolizes glucose into triacylglycerol (TAG) in the smallest number of steps. By visualizing the data this way, we observed a separate up-regulation of genes at different times instead of a concerted response. We also identified two metabolic paths that used less reactions than the one shown in KEGG and showed that the reactions were up-regulated during the experiment. The combination of analysis and visualization methods successfully analyzed time-course data, identified important metabolic pathways and provided new hypotheses for further research.
authors.affiliation: CBRC, National Institute of AIST, Tokyo, Japan.
authors.forename: Pui Shan
authors.initials: PS
authors.lastname: Wong
authors.affiliation: Center for iPS Research and Application, Kyoto University, Kyoto, Japan.
authors.forename: Michihiro
authors.initials: M
authors.lastname: Tanaka
authors.affiliation: Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan; JST, CREST, Sanbancho 5, Chiyoda-ku, Tokyo, Japan.
authors.forename: Yoshihiko
authors.initials: Y
authors.lastname: Sunaga
authors.affiliation: Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan.
authors.forename: Masayoshi
authors.initials: M
authors.lastname: Tanaka
authors.affiliation: Mitsubishi Research Institute, Inc., Tokyo, Japan.
authors.forename: Takeaki
authors.initials: T
authors.lastname: Taniguchi
authors.affiliation: Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan; JST, CREST, Sanbancho 5, Chiyoda-ku, Tokyo, Japan.
authors.forename: Tomoko
authors.initials: T
authors.lastname: Yoshino
authors.affiliation: Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan; JST, CREST, Sanbancho 5, Chiyoda-ku, Tokyo, Japan.
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Tanaka
authors.affiliation: CBRC, National Institute of AIST, Tokyo, Japan; Center for iPS Research and Application, Kyoto University, Kyoto, Japan.
authors.forename: Wataru
authors.initials: W
authors.lastname: Fujibuchi
authors.affiliation: CBRC, National Institute of AIST, Tokyo, Japan.
authors.forename: Sachiyo
authors.initials: S
authors.lastname: Aburatani
mesh_terms: D056804:Biofuels; D053898:Biosynthetic Pathways / Q000235:genetics; D017377:Diatoms / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks; D050356:Lipid Metabolism; D058086:Microalgae / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D056804:Biofuels