ATGC Transcriptomics: An application to annotate, integrate and analyze de-novo transcriptomic data

S. GONZÁLEZ; B. CLAVIJO; M. RIVAROLA; P. MORENO; P. FERNANDEZ; M. FARBER; N. PANIEGO

Belo Horizonte

Congreso; X Meeting ISCB Latin America; 2014

International Society of Computational Biology

Transcriptome analysis of species with non­reference genome involves the integration of de­novo assembly together with structural and functional annotation and other additional information, such as differential expression, genotypes or molecular markers. Also, with the increase in the volume of data, this creates an increase in complexity of the interpretation and analysis of results and generates the need for a software solution to manage, explore, integrate and visualize the results of different analysis. This solution has so far been lacking behind, especially for small groups and laboratories that perform these experiments without large data management capabilities. One approach, taken in this work, is the ability to store data orderly using modular database schema allows the users to create new hypothesis as result of the exploratory experiments or answer biological questions of interest. The Chado database [1], is a ontology driven and relational schema designed by Generic Model Organism Database (GMOD), to handle complex representations of biological knowledge. For non­informatics users to administer, manage and explore their database without a graphical interface help is complicated and not intuitive. Here we proposed ATGC a web application to visualize, explore, analyze and share de novo transcriptomic data generated by NGS platforms using a Chado database to store the data. It is an open source and free available application, with support to store information in several Chado modules and uses different ontologies to classify data and then explore this data using a ontology structure with graphics, searches and description tables