Blog
About

  • Record: found
  • Abstract: found
  • Article: found
Is Open Access

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species

Read this article at

Bookmark
      There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

      Abstract

      Tree species of the genus Eucalyptus are the most valuable and widely planted hardwoods in the world. Given the economic importance of Eucalyptus trees, much effort has been made towards the generation of specimens with superior forestry properties that can deliver high-quality feedstocks, customized to the industrýs needs for both cellulosic (paper) and lignocellulosic biomass production. In line with these efforts, large sets of molecular data have been generated by several scientific groups, providing invaluable information that can be applied in the development of improved specimens. In order to fully explore the potential of available datasets, the development of a public database that provides integrated access to genomic and transcriptomic data from Eucalyptus is needed. EUCANEXT is a database that analyses and integrates publicly available Eucalyptus molecular data, such as the E. grandis genome assembly and predicted genes, ESTs from several species and digital gene expression from 26 RNA-Seq libraries. The database has been implemented in a Fedora Linux machine running MySQL and Apache, while Perl CGI was used for the web interfaces. EUCANEXT provides a user-friendly web interface for easy access and analysis of publicly available molecular data from Eucalyptus species. This integrated database allows for complex searches by gene name, keyword or sequence similarity and is publicly accessible at http://www.lge.ibi.unicamp.br/eucalyptusdb. Through EUCANEXT, users can perform complex analysis to identify genes related traits of interest using RNA-Seq libraries and tools for differential expression analysis. Moreover, all the bioinformatics pipeline here described, including the database schema and PERL scripts, are readily available and can be applied to any genomic and transcriptomic project, regardless of the organism. Database URL: http://www.lge.ibi.unicamp.br/eucalyptusdb

      Related collections

      Most cited references 45

      • Record: found
      • Abstract: not found
      • Article: not found

      Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

        Bookmark
        • Record: found
        • Abstract: found
        • Article: found
        Is Open Access

        Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

        In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
          Bookmark
          • Record: found
          • Abstract: found
          • Article: not found

          Mapping and quantifying mammalian transcriptomes by RNA-Seq.

          We have mapped and quantified mouse transcriptomes by deeply sequencing them and recording how frequently each gene is represented in the sequence sample (RNA-Seq). This provides a digital measure of the presence and prevalence of transcripts from known and previously unknown genes. We report reference measurements composed of 41-52 million mapped 25-base-pair reads for poly(A)-selected RNA from adult mouse brain, liver and skeletal muscle tissues. We used RNA standards to quantify transcript prevalence and to test the linear range of transcript detection, which spanned five orders of magnitude. Although >90% of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3' untranscribed regions, as well as new candidate microRNA precursors. RNA splice events, which are not readily measured by standard gene expression microarray or serial analysis of gene expression methods, were detected directly by mapping splice-crossing sequence reads. We observed 1.45 x 10(5) distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices.
            Bookmark

            Author and article information

            Affiliations
            [1 ]Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
            [2 ]Laboratório Central de Tecnologias de Alto Desempenho (LaCTAD), Universidade Estadual de Campinas, Campinas, SP, Brasil
            [3 ]Centro Nacional de Processamento de Alto Desempenho em São Paulo (CENAPAD), Universidade Estadual de Campinas, Campinas, SP, Brasil
            Author notes
            [* ] Corresponding author: Tel: 00-55-19-3521-6238; Fax: 00-55-19-3521-6235; Email: goncalo@ 123456unicamp.br
            [†]

            Citation details: Nascimento,L.C., Salazar,M.M., Lepikson-Neto,J., et al. EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species. Database (2017) Vol. 2017: article ID bax079; doi:10.1093/database/bax079

            Journal
            Database (Oxford)
            Database (Oxford)
            databa
            Database: The Journal of Biological Databases and Curation
            Oxford University Press
            1758-0463
            2017
            24 October 2017
            24 October 2017
            : 2017
            29220468
            5737058
            10.1093/database/bax079
            bax079
            © The Author(s) 2017. Published by Oxford University Press.

            This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

            Counts
            Pages: 12
            Product
            Categories
            Database Tool

            Bioinformatics & Computational biology

            Comments

            Comment on this article