![]() Lee H, Schatz MC (2012) Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score. (2012) Analyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the metaxpress consortium. Schurmann C, Heim K, Schillert A, Blankenberg S, Carstensen M, Dörr M, et al. (2010) A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. 10.1038/nature11405īarbosa-Morais NL, Dunning MJ, Samarajiwa SA, Darot JF, Ritchie ME, Lynch AG, et al. (2012) An anatomically comprehensive atlas of the adult human brain transcriptome. Hawrylycz MJ, Lein ES, Guillozet-Bongaarts AL, Shen EH, Ng L, Miller JA, et al. Technology, statistical tools and biological knowledge in general have evolved over the past ten years and it is now. Pruitt KD, Tatusova T, Brown GR, Maglott DR (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Microarrays are tools to study the expression profile of an entire genome. array: Suppose, for example, z is a vector of 1500 elements. The Re-Annotator pipeline is freely available at along with re-annotated files for Illumina microarrays HumanHT-12 v3/v4 and MouseRef-8 v2. Example: the expression values for 10000 genes for 30 tissue biopsies is a numeric matrix with 10000 rows and 30 columns. A thorough re-annotation of probe information is crucial to any microarray analysis. 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. 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. The Re-Annotator uses a custom-built mRNA reference database to identify the positions of gene expression array probe sequences. It is primarily designed for gene expression microarrays but can also be adapted to other types of microarrays. Here, we present the Re-Annotator, a re-annotation pipeline for microarray probe sequences. However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases. An accurate mapping of the array probes is essential to generate reliable biological findings. Microarray technologies are established approaches for high throughput gene expression, methylation and genotyping analysis. ![]()
0 Comments
Leave a Reply. |
Details
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |