RNA-Seq Viewer is a new mobile application built for iOS to provide biologists a new user experience in interrogating large-scale Next-Generation-Sequencing (NGS) data intuitively on the iPad or iPhone. In its initial release, we focus on the visualization of RNA-Seq data from TCGA (The Cancer Genome Atlas). TCGA is a comprehensive and coordinated effort to accelerate the understanding of the molecular basis of cancer through the utilization of large-scale sequencing NGS platforms. Here, human RefSeq gene coordinates are obtained from NCBI (National Center for Biotechnology Information) and integrated with the RNA-Seq expression information to provide the human cancer cell transcriptome landscapes. Unique features of this bioinformatic mobile APP include:
1. Gene expression information (RPKM value) of individual patient with brief clinical annotation is visualized and displayed on the chromosome landscapes.
2. RNA-Seq data from over 2,500 cancer patients on nine different prevalent cancer types were retrieved from TCGA and available for download.
3. Users can further browse and interrogate differentially expressed genes by zooming into regions of particular interest.
4. Users can mark the interested cancer sample information for subsequent analysis and for sharing with other biomedical researchers.
5. Detailed gene information could be navigated directly from NCBI GenBank database.
6. Users can establish their own NGS RNA-Seq data file (using the ‘user.agv’ template file) for visualization and interrogation.
Future systems biology integration at the single gene level with methylation data, CNV data and miRNA expression data would be anticipated. Any suggestions and comments are welcome, please contact: Dr. Wen-chang Lin -- [email protected]