SMART-RDA: A Galaxy Workflow for RNA-Seq Data Analysis

RNA-seq using the Next Generation Sequencing (NGS) approach is a common technology to analyze large-scale RNA transcript data for gene expression studies. However, an appropriate bioinformatics tool is needed to analyze a large amount of transcriptomes data from RNA-seq experiment. The aim of this study was to construct a system that can be easily applied to analyze RNA-seq data. RNA-seq analysis tool as SMART-RDA was constructed in this study. It is a computational workflow based on Galaxy framework to be used for analyzing RNA-seq raw data into gene expression information. This workflow was adapted from a well-known Tuxedo Protocol for RNA-seq analysis with some modifications. Expression value from each transcriptome was quantitatively stated as Fragments Per Kilobase of exon per Million fragments (FPKM). RNA-seq data of sterile and fertile oil palm (Pisifera) pollens derived from Sequence Read Archive (SRA) NCBI were used to test this workflow in local facility Galaxy server. The results showed that differentially gene expression in pollens might be responsible for sterile and fertile characteristics in palm oil Pisifera.Keywords: FPKM; Galaxy workflow; Gene expression; RNA sequencing

Biological Network Analysis of Genes Involve in Embryogenesis of Oil Palm using ClueGO

The application of DNA sequencing technologies has a major impact on molecular biology, especially in understanding genes interaction in a certain condition. Due to a large number of genes produced by this high-throughput technology, a proper analysis tool is needed for data interpretation. ClueGO is a bioinformatics tool, an easy to use Cytoscape plug-in that strongly improves biological function interpretation of genes. It analyzes a cluster or comparing two clusters and comprehensively visualizes their group functions. This tool is applied to identify biological networks of genes involved in embryogenesis of oil palm, the most critical phase in oil palm tissue culture process. Two ESTs sequencing data from the GenBank database under accession number EY396120-EY413718 and DW247764-DW248770 were used in this study. Fifty-two and one hundred eight groups of genes were identified using biological process in Gene Ontology setting from the database of EY396120-EY413718 and DW247764-DW248770, respectively. Thirty-one groups of genes were consistently occurred in both ESTs. According to the literature, these genes play an important role in cell formations and developments, stresses and stimulus responses, photosynthesis and metabolic processes that indicate the involvement of these groups of genes in oil palm embryogenesis processes. ClueGO is the appropriate tool to analyze a large data set of genes in a specific condition, such as embryogenesis of oil palm. Keywords: callus embryogenesis; Cytoscape plug-in; DNA sequencing; expressed sequence tag; KEGG pathway