原创力文档anyexpress integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithmanyexpress集成工具包跨平台的基因表达数据的分析利用快速间隔匹配算法.pdfVIP
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anyexpress integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithmanyexpress集成工具包跨平台的基因表达数据的分析利用快速间隔匹配算法
Kim et al. BMC Bioinformatics 2011, 12:75
/1471-2105/12/75
SOFTWARE Open Access
AnyExpress: Integrated toolkit for analysis of
cross-platform gene expression data using a fast
interval matching algorithm
1 1 1,2 3 1,2*
Jihoon Kim , Kiltesh Patel , Hyunchul Jung , Winston P Kuo and Lucila Ohno-Machado
Abstract
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such as reference genome, transcriptome database, and SNP, which are often erroneous or outdated, that the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, respectivel
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