PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data

<p>Abstract</p> <p>Background</p> <p>Nowadays, microarray gene expression analysis is a widely used technology that scientists handle but whose final interpretation usually requires the participation of a specialist. The need for this participation is due to the requirement of some background in statistics that most users lack or have a very vague notion of. Moreover, programming skills could also be essential to analyse these data. An interactive, easy to use application seems therefore necessary to help researchers to extract full information from data and analyse them in a simple, powerful and confident way.</p> <p>Results</p> <p>PreP+07 is a standalone Windows XP application that presents a friendly interface for spot filtration, inter- and intra-slide normalization, duplicate resolution, dye-swapping, error removal and statistical analyses. Additionally, it contains two unique implementation of the procedures – double scan and Supervised Lowess-, a complete set of graphical representations – MA plot, RG plot, QQ plot, PP plot, PN plot – and can deal with many data formats, such as tabulated text, GenePix GPR and ArrayPRO. PreP+07 performance has been compared with the equivalent functions in Bioconductor using a tomato chip with 13056 spots. The number of differentially expressed genes considering p-values coming from the PreP+07 and Bioconductor Limma packages were statistically identical when the data set was only normalized; however, a slight variability was appreciated when the data was both normalized and scaled.</p> <p>Conclusion</p> <p>PreP+07 implementation provides a high degree of freedom in selecting and organizing a small set of widely used data processing protocols, and can handle many data formats. Its reliability has been proven so that a laboratory researcher can afford a statistical pre-processing of his/her microarray results and obtain a list of differentially expressed genes using PreP+07 without any programming skills. All of this gives support to scientists that have been using previous PreP releases since its first version in 2003.</p

CIBERER : Spanish national network for research on rare diseases: A highly productive collaborative initiative

Altres ajuts: Instituto de Salud Carlos III (ISCIII); Ministerio de Ciencia e Innovación.CIBER (Center for Biomedical Network Research; Centro de Investigación Biomédica En Red) is a public national consortium created in 2006 under the umbrella of the Spanish National Institute of Health Carlos III (ISCIII). This innovative research structure comprises 11 different specific areas dedicated to the main public health priorities in the National Health System. CIBERER, the thematic area of CIBER focused on rare diseases (RDs) currently consists of 75 research groups belonging to universities, research centers, and hospitals of the entire country. CIBERER's mission is to be a center prioritizing and favoring collaboration and cooperation between biomedical and clinical research groups, with special emphasis on the aspects of genetic, molecular, biochemical, and cellular research of RDs. This research is the basis for providing new tools for the diagnosis and therapy of low-prevalence diseases, in line with the International Rare Diseases Research Consortium (IRDiRC) objectives, thus favoring translational research between the scientific environment of the laboratory and the clinical setting of health centers. In this article, we intend to review CIBERER's 15-year journey and summarize the main results obtained in terms of internationalization, scientific production, contributions toward the discovery of new therapies and novel genes associated to diseases, cooperation with patients' associations and many other topics related to RD research

SNPs_fixed

SNPs fixed in boscai from Portugal and Spai

Data from: De novo transcriptome assembly and polymorphism detection in two highly divergent evolutionary units of Bosca's newt (Lissotriton boscai) endemic to the Iberian Peninsula

This article reports the de novo transcriptomes of two highly divergent evolutionary units of the Iberian endemic Bosca’s newt, Lissotriton boscai. These two units are distributed allopatrically but meet in areas of secondary contact in central-southwestern coastal region of Portugal. The resources we provide include the raw sequence reads, the assembled transcripts and SNPs called for both lineages

boscai_spain_contigs

Contigs generated by Trinity assembler from all the reads belonging to boscai from Spai

SNPs_shared_between_boscai_portugal_and_boscai_spain

SNPs shared between boscai from Portugal and boscai from Spai

boscai_spain_annotation

Annotations generated by Sma3s software for contigs belonging to boscai from Spai

boscai_portugal_annotation

Annotations generated by Sma3s software for contigs belonging to boscai from Portuga

boscai_portugal_contigs

Contigs generated by Trinity assembler from all the reads belonging to boscai from Portugal