Re-Annotator: Annotation Pipeline for Microarray Probe Sequences.
Re-Annotator: Annotation Pipeline for Microarray Probe Sequences.
复制标题
DOI：
10.1371/journal.pone.0139516
复制
发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Altmann A
中科院分区：
文献类型：
--
作者：
Arloth J;Bader DM;Röh S;Altmann A
微阵列技术是用于高通量基因表达、甲基化和基因分型分析的既定方法。阵列探针的准确映射对于产生可靠的生物学发现是必不可少的。然而，微阵列平台的制造商通常提供不完整和过时的注释表，其通常依赖于与最新序列数据库有很大不同的较旧的基因组和转录组版本。在这里，我们提出了重新注释器，微阵列探针序列的重新注释管道。它主要设计用于基因表达微阵列，但也可以适用于其他类型的微阵列。Re-Annotator使用定制的mRNA参考数据库来识别基因表达阵列探针序列的位置。我们将Re-Annotator应用于Illumina Human-HT 12 v4微阵列平台，发现大约四分之一（25%）的探针与制造商的注释不同。在对实验基因表达数据的进一步计算实验中，我们将Re-Annotator与另一种探针重新注释工具ReMOAT进行了比较，发现Re-Annotator提供了改进的微阵列探针重新注释。探针信息的彻底重新注释对于任何微阵列分析都至关重要。Re-Annotator流水线可在http://sourceforge.net/projects/reannotator沿着免费获得，同时提供Illumina微阵列HumanHT-12 v3/v4和MouseRef-8 v2的重新注释文件。
Microarray technologies are established approaches for high throughput gene expression, methylation and genotyping analysis. An accurate mapping of the array probes is essential to generate reliable biological findings. However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases. Here, we present the Re-Annotator, a re-annotation pipeline for microarray probe sequences. It is primarily designed for gene expression microarrays but can also be adapted to other types of microarrays. The Re-Annotator uses a custom-built mRNA reference database to identify the positions of gene expression array probe sequences. We applied Re-Annotator to the Illumina Human-HT12 v4 microarray platform and found that about one quarter (25%) of the probes differed from the manufacturer’s annotation. In further computational experiments on experimental gene expression data, we compared Re-Annotator to another probe re-annotation tool, ReMOAT, and found that Re-Annotator provided an improved re-annotation of microarray probes. A thorough re-annotation of probe information is crucial to any microarray analysis. The Re-Annotator pipeline is freely available at http://sourceforge.net/projects/reannotator along with re-annotated files for Illumina microarrays HumanHT-12 v3/v4 and MouseRef-8 v2.