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and genotyping analysis.However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases.It is primarily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 However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases.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


Comparison between Re-Annotator and ReMOAT on HumanHT-12 v4 probe sequences.(A) Venn diagram representing the overlap of transcripts annotated with ReMOAT and Re-Annotator. A total of 5% of the probe sequences were annotated with different genes by Re-Annotator and ReMOAT. (B) Bar graph detailing the exclusion reason for probes included by ReMOAT but excluded by Re-Annotator.
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pone.0139516.g004: Comparison between Re-Annotator and ReMOAT on HumanHT-12 v4 probe sequences.(A) Venn diagram representing the overlap of transcripts annotated with ReMOAT and Re-Annotator. A total of 5% of the probe sequences were annotated with different genes by Re-Annotator and ReMOAT. (B) Bar graph detailing the exclusion reason for probes included by ReMOAT but excluded by Re-Annotator.

Mentions: Comparing Re-Annotator to ReMOAT, another re-annotation tool, we found that 86.3% (n = 29,759) of probe sequences annotated as "good" by ReMOAT (quality equal to”Perfect” and “Good”; n = 34,476 sequences) were also classified as “good” probes by Re-Annotator (Fig 4A). However, 5% (n = 1,532) of these 29,795 array probes received different annotations by the two tools. A total of 4,717 probes, which were annotated as “good” by ReMOAT, were excluded by Re-Annotator due to alignments in intergenic regions (63.7%), multiple different hits in the mRNA reference (26%) and no alignment (10.3%) (Fig 4B).


Re-Annotator: Annotation Pipeline for Microarray Probe Sequences.

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

Comparison between Re-Annotator and ReMOAT on HumanHT-12 v4 probe sequences.(A) Venn diagram representing the overlap of transcripts annotated with ReMOAT and Re-Annotator. A total of 5% of the probe sequences were annotated with different genes by Re-Annotator and ReMOAT. (B) Bar graph detailing the exclusion reason for probes included by ReMOAT but excluded by Re-Annotator.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139516.g004: Comparison between Re-Annotator and ReMOAT on HumanHT-12 v4 probe sequences.(A) Venn diagram representing the overlap of transcripts annotated with ReMOAT and Re-Annotator. A total of 5% of the probe sequences were annotated with different genes by Re-Annotator and ReMOAT. (B) Bar graph detailing the exclusion reason for probes included by ReMOAT but excluded by Re-Annotator.
Mentions: Comparing Re-Annotator to ReMOAT, another re-annotation tool, we found that 86.3% (n = 29,759) of probe sequences annotated as "good" by ReMOAT (quality equal to”Perfect” and “Good”; n = 34,476 sequences) were also classified as “good” probes by Re-Annotator (Fig 4A). However, 5% (n = 1,532) of these 29,795 array probes received different annotations by the two tools. A total of 4,717 probes, which were annotated as “good” by ReMOAT, were excluded by Re-Annotator due to alignments in intergenic regions (63.7%), multiple different hits in the mRNA reference (26%) and no alignment (10.3%) (Fig 4B).

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.