SUMMARY: Development of effective tools such as oligo-microarrays and next-generation sequencing methods for monitoring gene expression on a large scale has resulted in the discovery of gene signatures with prognostic/predictive value in various malignant neoplastic diseases. However, with the exponential growth of gene expression databases, biologists are faced with the challenge of extracting useful information from these repositories. Here, we present a software package, BioPlat (Biomarkers Platform), which allows biologists to identify novel prognostic and predictive cancer biomarkers based on the data mining of gene expression signatures and gene expression profiling databases. BioPlat has been designed as an easy-to-use and flexible desktop software application, which provides a set of analytical tools related to data extraction, preprocessing, filtering, gene expression signature calculation, in silico validation, feature selection and annotation that leverage the integration and reuse of gene expression signatures in the context of follow-up data. AVAILABILITY AND IMPLEMENTATION: BioPlat is a platform-independent software implemented in Java and supported on GNU/Linux and MS Windows, which is freely available for download at http://www.cancergenomics.net.
SUMMARY: Development of effective tools such as oligo-microarrays and next-generation sequencing methods for monitoring gene expression on a large scale has resulted in the discovery of gene signatures with prognostic/predictive value in various malignant neoplastic diseases. However, with the exponential growth of gene expression databases, biologists are faced with the challenge of extracting useful information from these repositories. Here, we present a software package, BioPlat (Biomarkers Platform), which allows biologists to identify novel prognostic and predictive cancer biomarkers based on the data mining of gene expression signatures and gene expression profiling databases. BioPlat has been designed as an easy-to-use and flexible desktop software application, which provides a set of analytical tools related to data extraction, preprocessing, filtering, gene expression signature calculation, in silico validation, feature selection and annotation that leverage the integration and reuse of gene expression signatures in the context of follow-up data. AVAILABILITY AND IMPLEMENTATION: BioPlat is a platform-independent software implemented in Java and supported on GNU/Linux and MS Windows, which is freely available for download at http://www.cancergenomics.net.
Authors: Jonatan Taminau; David Steenhoff; Alain Coletta; Stijn Meganck; Cosmin Lazar; Virginie de Schaetzen; Robin Duque; Colin Molter; Hugues Bersini; Ann Nowé; David Y Weiss Solís Journal: Bioinformatics Date: 2011-09-21 Impact factor: 6.937
Authors: Robert C Gentleman; Vincent J Carey; Douglas M Bates; Ben Bolstad; Marcel Dettling; Sandrine Dudoit; Byron Ellis; Laurent Gautier; Yongchao Ge; Jeff Gentry; Kurt Hornik; Torsten Hothorn; Wolfgang Huber; Stefano Iacus; Rafael Irizarry; Friedrich Leisch; Cheng Li; Martin Maechler; Anthony J Rossini; Gunther Sawitzki; Colin Smith; Gordon Smyth; Luke Tierney; Jean Y H Yang; Jianhua Zhang Journal: Genome Biol Date: 2004-09-15 Impact factor: 13.583
Authors: Tanya Barrett; Stephen E Wilhite; Pierre Ledoux; Carlos Evangelista; Irene F Kim; Maxim Tomashevsky; Kimberly A Marshall; Katherine H Phillippy; Patti M Sherman; Michelle Holko; Andrey Yefanov; Hyeseung Lee; Naigong Zhang; Cynthia L Robertson; Nadezhda Serova; Sean Davis; Alexandra Soboleva Journal: Nucleic Acids Res Date: 2012-11-27 Impact factor: 16.971
Authors: Aedín C Culhane; Markus S Schröder; Razvan Sultana; Shaita C Picard; Enzo N Martinelli; Caroline Kelly; Benjamin Haibe-Kains; Misha Kapushesky; Anne-Alyssa St Pierre; William Flahive; Kermshlise C Picard; Daniel Gusenleitner; Gerald Papenhausen; Niall O'Connor; Mick Correll; John Quackenbush Journal: Nucleic Acids Res Date: 2011-11-21 Impact factor: 16.971
Authors: Gabriella Rustici; Nikolay Kolesnikov; Marco Brandizi; Tony Burdett; Miroslaw Dylag; Ibrahim Emam; Anna Farne; Emma Hastings; Jon Ison; Maria Keays; Natalja Kurbatova; James Malone; Roby Mani; Annalisa Mupo; Rui Pedro Pereira; Ekaterina Pilicheva; Johan Rung; Anjan Sharma; Y Amy Tang; Tobias Ternent; Andrew Tikhonov; Danielle Welter; Eleanor Williams; Alvis Brazma; Helen Parkinson; Ugis Sarkans Journal: Nucleic Acids Res Date: 2012-11-27 Impact factor: 16.971