title: ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data.
abstract: BACKGROUND
  In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for evaluating differential gene expression by digital measurements. The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis. This problem is especially significant for small research groups working with non-model species.
  
  
  RESULTS
  We developed a web-based application, called ATGC transcriptomics, with a flexible and adaptable interface that allows users to work with new generation sequencing (NGS) transcriptomic analysis results using an ontology-driven database. This new application simplifies data exploration, visualization, and integration for a better comprehension of the results.
  
  
  CONCLUSIONS
  ATGC transcriptomics provides access to non-expert computer users and small research groups to a scalable storage option and simple data integration, including database administration and management. The software is freely available under the terms of GNU public license at http://atgcinta.sourceforge.net .
authors.affiliation: Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires, Argentina. gonzalez.sergio@inta.gob.ar.
authors.forename: Sergio
authors.initials: S
authors.lastname: Gonzalez
authors.affiliation: Earlham Institute, Norwich Research Park, Norwich, NR4 7UG, UK.
authors.forename: Bernardo
authors.initials: B
authors.lastname: Clavijo
authors.affiliation: Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires, Argentina. rivarola.maximo@inta.gob.ar.|Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires, C1425FQB, Argentina. rivarola.maximo@inta.gob.ar.
authors.forename: Máximo
authors.initials: M
authors.lastname: Rivarola
authors.affiliation: Instituto de Ingeniería Biomédica, Facultad de Ingeniería, Universidad de Buenos Aires, Buenos Aires, Argentina.
authors.forename: Patricio
authors.initials: P
authors.lastname: Moreno
authors.affiliation: Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires, Argentina.|Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires, C1425FQB, Argentina.|Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina.
authors.forename: Paula
authors.initials: P
authors.lastname: Fernandez
authors.affiliation: Computational Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain.
authors.forename: Joaquín
authors.initials: J
authors.lastname: Dopazo
authors.affiliation: Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires, Argentina.|Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires, C1425FQB, Argentina.
authors.forename: Norma
authors.initials: N
authors.lastname: Paniego
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D014584:User-Computer Interface
keywords: Data integration; De novo transcriptomics; Ontology storage; Web application