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Re-Annotator: Annotation Pipeline for Microarray Probe Sequences.

Arloth J, Bader DM, Röh S, Altmann A - PLoS ONE (2015)

Bottom Line: Microarray technologies are established approaches for high throughput gene expression, methylation and genotyping analysis.However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases.It is primarily designed for gene expression microarrays but can also be adapted to other types of microarrays.

View Article: PubMed Central - PubMed

Affiliation: Translational Research Department, Max Planck Institute of Psychiatry, Kraepelinstrasse 2-10, 80804, Munich, Germany.

ABSTRACT
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 However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases.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.

No MeSH data available.


Results of the re-annotation of Illumina MouseRef-8 v2 probe sequences.(A) Barplot of the alignment basis. The left bar represents the array probe sequences that could be aligned to the in silico mRNA reference database. The middle bar represents sequences that were aligned to the whole genome reference subdivided into genic and intergenic alignments. The right bar represents unaligned sequences. Histograms showing (B) the number of mismatches between probe sequence and reference and (C) the number of equally top scoring best hits per probe sequence.
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pone.0139516.g003: Results of the re-annotation of Illumina MouseRef-8 v2 probe sequences.(A) Barplot of the alignment basis. The left bar represents the array probe sequences that could be aligned to the in silico mRNA reference database. The middle bar represents sequences that were aligned to the whole genome reference subdivided into genic and intergenic alignments. The right bar represents unaligned sequences. Histograms showing (B) the number of mismatches between probe sequence and reference and (C) the number of equally top scoring best hits per probe sequence.

Mentions: Additionally, we analyzed the Illumina MouseRef-8 v2 probe sequences (n = 25,697) using our Re-Annotator pipeline. Almost all probes were aligned (99.4%; Fig 3A; Table 1) to either the mRNA reference database (n = 24,994) or the genome sequence (n = 548) and passed the post-processing filter (Table 1). 97.9% of all post-processed array probe sequences were aligned without mismatches (Fig 3B; Table 1) and 93.5% mapped to a single region with only 14 probes having five or more hits per probe (Fig 3C; Table 1). The successful re-annotation of the mouse microarray can be explained by the reduced array content to only RefSeq genes, providing good transcriptomic annotation quality.


Re-Annotator: Annotation Pipeline for Microarray Probe Sequences.

Arloth J, Bader DM, Röh S, Altmann A - PLoS ONE (2015)

Results of the re-annotation of Illumina MouseRef-8 v2 probe sequences.(A) Barplot of the alignment basis. The left bar represents the array probe sequences that could be aligned to the in silico mRNA reference database. The middle bar represents sequences that were aligned to the whole genome reference subdivided into genic and intergenic alignments. The right bar represents unaligned sequences. Histograms showing (B) the number of mismatches between probe sequence and reference and (C) the number of equally top scoring best hits per probe sequence.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591122&req=5

pone.0139516.g003: Results of the re-annotation of Illumina MouseRef-8 v2 probe sequences.(A) Barplot of the alignment basis. The left bar represents the array probe sequences that could be aligned to the in silico mRNA reference database. The middle bar represents sequences that were aligned to the whole genome reference subdivided into genic and intergenic alignments. The right bar represents unaligned sequences. Histograms showing (B) the number of mismatches between probe sequence and reference and (C) the number of equally top scoring best hits per probe sequence.
Mentions: Additionally, we analyzed the Illumina MouseRef-8 v2 probe sequences (n = 25,697) using our Re-Annotator pipeline. Almost all probes were aligned (99.4%; Fig 3A; Table 1) to either the mRNA reference database (n = 24,994) or the genome sequence (n = 548) and passed the post-processing filter (Table 1). 97.9% of all post-processed array probe sequences were aligned without mismatches (Fig 3B; Table 1) and 93.5% mapped to a single region with only 14 probes having five or more hits per probe (Fig 3C; Table 1). The successful re-annotation of the mouse microarray can be explained by the reduced array content to only RefSeq genes, providing good transcriptomic annotation quality.

Bottom Line: Microarray technologies are established approaches for high throughput gene expression, methylation and genotyping analysis.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.It is primarily designed for gene expression microarrays but can also be adapted to other types of microarrays.

View Article: PubMed Central - PubMed

Affiliation: Translational Research Department, Max Planck Institute of Psychiatry, Kraepelinstrasse 2-10, 80804, Munich, Germany.

ABSTRACT
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.

No MeSH data available.