IC4R017-RNA-Seq-2014-24518221

Project Title

Time-series RNA-seq analysis package (TRAP) and its application to the analysis of rice, Oryza sativa L. ssp. Japonica, upon drought stress

The high throughput RNA sequencing(RNA-seq) technique has advantages over microarray technique such as the decreased noise level and more replicable results ,compared to microarrays. For this reason, the number of time-series RNA-seq data sets in the public domain has increased dramatically over the past few years.
The main issue with RNA-seq is to handle sequencing data that is much bigger than microarray data.The researchers developed a comprehensive package, Time-series RNA-seq Analysis Package (TRAP), for analyzing time series transcriptome data. There have been many packages developed for analyzing time-series gene expression data. The most widely used technique is to identify DEGs. Packages for finding DEGs from time-series data include SAM , LIMMA ,EDGE , maSigPro and BETR .However, most of them are developed for microarray data and they assume that gene expression follows normal distribution. Users with RNA-seq data,therefore, should perform additional conversion process or use the certain type of distribution (e.g., Poisson or Binomial) which needs

further validation.

Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea
Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
Department of Biomedical Sciences, Sunmoon University, Asan 336-708, Republic of Korea