BACKGROUND: Cross-platform analysis of gene express data requires multiple, intricate processes at different layers with various platforms. However, existing tools handle only a single platform and are not flexible enough to support custom changes, which arise from the new statistical methods, updated versions of reference data, and better platforms released every month or year. Current tools are so tightly coupled with reference information, such as reference genome, transcriptome database, and SNP, which are often erroneous or outdated, that the output results are incorrect and misleading. RESULTS: We developed AnyExpress, a software package that combines cross-platform gene expression data using a fast interval-matching algorithm. Supported platforms include next-generation-sequencing technology, microarray, SAGE, MPSS, and more. Users can define custom target transcriptome database references for probe/read mapping in any species, as well as criteria to remove undesirable probes/reads. AnyExpress offers scalable processing features such as binding, normalization, and summarization that are not present in existing software tools. As a case study, we applied AnyExpress to published Affymetrix microarray and Illumina NGS RNA-Seq data from human kidney and liver. The mean of within-platform correlation coefficient was 0.98 for within-platform samples in kidney and liver, respectively. The mean of cross-platform correlation coefficients was 0.73. These results confirmed those of the original and secondary studies. Applying filtering produced higher agreement between microarray and NGS, according to an agreement index calculated from differentially expressed genes. CONCLUSION: AnyExpress can combine cross-platform gene expression data, process data from both open- and closed-platforms, select a custom target reference, filter out undesirable probes or reads based on custom-defined biological features, and perform quantile-normalization with a large number of microarray samples. AnyExpress is fast, comprehensive, flexible, and freely available at http://anyexpress.sourceforge.net.
BACKGROUND: Cross-platform analysis of gene express data requires multiple, intricate processes at different layers with various platforms. However, existing tools handle only a single platform and are not flexible enough to support custom changes, which arise from the new statistical methods, updated versions of reference data, and better platforms released every month or year. Current tools are so tightly coupled with reference information, such as reference genome, transcriptome database, and SNP, which are often erroneous or outdated, that the output results are incorrect and misleading. RESULTS: We developed AnyExpress, a software package that combines cross-platform gene expression data using a fast interval-matching algorithm. Supported platforms include next-generation-sequencing technology, microarray, SAGE, MPSS, and more. Users can define custom target transcriptome database references for probe/read mapping in any species, as well as criteria to remove undesirable probes/reads. AnyExpress offers scalable processing features such as binding, normalization, and summarization that are not present in existing software tools. As a case study, we applied AnyExpress to published Affymetrix microarray and Illumina NGS RNA-Seq data from human kidney and liver. The mean of within-platform correlation coefficient was 0.98 for within-platform samples in kidney and liver, respectively. The mean of cross-platform correlation coefficients was 0.73. These results confirmed those of the original and secondary studies. Applying filtering produced higher agreement between microarray and NGS, according to an agreement index calculated from differentially expressed genes. CONCLUSION: AnyExpress can combine cross-platform gene expression data, process data from both open- and closed-platforms, select a custom target reference, filter out undesirable probes or reads based on custom-defined biological features, and perform quantile-normalization with a large number of microarray samples. AnyExpress is fast, comprehensive, flexible, and freely available at http://anyexpress.sourceforge.net.
Authors: Monica Benito; Joel Parker; Quan Du; Junyuan Wu; Dong Xiang; Charles M Perou; J S Marron Journal: Bioinformatics Date: 2004-01-01 Impact factor: 6.937
Authors: Sek Won Kong; Kyu-Baek Hwang; Richard D Kim; Byoung-Tak Zhang; Steven A Greenberg; Isaac S Kohane; Peter J Park Journal: Bioinformatics Date: 2005-01-31 Impact factor: 6.937
Authors: Manhong Dai; Pinglang Wang; Andrew D Boyd; Georgi Kostov; Brian Athey; Edward G Jones; William E Bunney; Richard M Myers; Terry P Speed; Huda Akil; Stanley J Watson; Fan Meng Journal: Nucleic Acids Res Date: 2005-11-10 Impact factor: 16.971
Authors: Francesco Ferrari; Stefania Bortoluzzi; Alessandro Coppe; Alexandra Sirota; Marilyn Safran; Michael Shmoish; Sergio Ferrari; Doron Lancet; Gian Antonio Danieli; Silvio Bicciato Journal: BMC Bioinformatics Date: 2007-11-15 Impact factor: 3.169
Authors: Lucila Ohno-Machado; Vineet Bafna; Aziz A Boxwala; Brian E Chapman; Wendy W Chapman; Kamalika Chaudhuri; Michele E Day; Claudiu Farcas; Nathaniel D Heintzman; Xiaoqian Jiang; Hyeoneui Kim; Jihoon Kim; Michael E Matheny; Frederic S Resnic; Staal A Vinterbo Journal: J Am Med Inform Assoc Date: 2011-11-10 Impact factor: 4.497
Authors: Caroline M Nievergelt; Allison E Ashley-Koch; Shareefa Dalvie; Michael A Hauser; Rajendra A Morey; Alicia K Smith; Monica Uddin Journal: Biol Psychiatry Date: 2018-02-02 Impact factor: 13.382