Bioinformatic approach for transcriptomics: integration of gene expression data based on RNA-seq with tissue localization

Abstract

One of the main challenges in current system biology research comes when different types of data must be accessed from various sources, metrics and visualization and analysis tools. The challenge increases when it comes to genetics and transcriptomics, in which, for most experiments, genes employ different naming identification based on the genome version, data normalization uses different protocols and data is compiled using different techniques. Accordingly, there is a need for an analytical-visual tool for cientific support which works as a research platform that incorporates all compiled data and provides integrated search, analysis and visualization features within a single platform, providing the latest and comprehensible data available. In this thesis, we present MtView; https://mtview.herokuapp.com/, a web tool for exploring multiple research levels of the legume plant Medicago truncatula and its nitrogen-fixing symbiotic interaction with the bacterium Sinorhizobium meliloti through a simple user interface. The app connects with various publicly available web services containing gene transcriptome, genome, proteome, interactome, tissue localization and 3D molecular structure for around the 70.000 genes expressed in the aforementioned legume.