BioPlat: a software for human cancer biomarker discovery

BUTTI M; CHANFREAU H; MARTINEZ D; GARCÍA D; LACUNZA E; ABBA MC

BIOINFORMATICS (OXFORD, ENGLAND)

OXFORD UNIV PRESS

Lugar: Oxford; Año: 2014 p. 1 - 3

1367-4803

Summary: Development of effective tools such as oligo-microarraysand next-generation sequencing methods for monitoring gene expres-sion on a large scale has resulted in the discovery of gene signatureswith prognostic/predictive value in various malignant neoplastic dis-eases. However, with the exponential growth of gene expression data-bases, biologists are faced with the challenge of extracting usefulinformation from these repositories. Here, we present a software pack-age, BioPlat (Biomarkers Platform), which allows biologists to identifynovel prognostic and predictive cancer biomarkers based on the datamining of gene expression signatures and gene expression profilingdatabases. BioPlat has been designed as an easy-to-use and flexibledesktop software application, which provides a set of analytical toolsrelated to data extraction, preprocessing, filtering, gene expressionsignature calculation, in silico validation, feature selection and anno-tation that leverage the integration and reuse of gene expression sig-natures in the context of follow-up data.Availability and implementation: BioPlat is a platform-independentsoftware implemented in Java and supported on GNU/Linux and MSWindows, which is freely available for download at http://www.cancergenomics.net.