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and genotyping analysis.However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases.It is primarily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 However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases.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


USCS genome browser graphic for the human ABCA9 gene.The gene is located on chromosome 9; the targeting Illumina probe is ILMN_1651396. Custom tracks represent the probe sequences annotated by (A) the Re-Annotator and (B) manufacturer and ReMOAT.
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pone.0139516.g006: USCS genome browser graphic for the human ABCA9 gene.The gene is located on chromosome 9; the targeting Illumina probe is ILMN_1651396. Custom tracks represent the probe sequences annotated by (A) the Re-Annotator and (B) manufacturer and ReMOAT.

Mentions: A precise annotation of microarray probe sequences is essential for accurate biological findings and replicability. In this work, we present a pipeline to re-annotate probe sequences of gene expression microarrays using a custom-built mRNA reference and applied it to three Illumina BeadChip arrays (Human HT-12 v3, v4 and MouseRef-8 v2). The re-annotation revealed that indeed one quarter of the array probes were incompletely or incorrectly annotated by the manufacturer. A source of such mis-annotation may be due to changes in genome assembly or changes in exon/intron boundaries since the original design of the chip. Over 21% of re-annotated probes were assigned to different genes as given by the manufacturer. For example, three of the five Illumina HumanHT-12 v4 array probe sequences illustrated in Fig 5 all perfectly re-annotated within the first or second exon of the human gene ISCA1 on chromosome 9 using the Re-Annotator. Originally these probes were annotated on chromosome 5 within an intergenic region (Fig 5). A reason for this discrepancy was that the probe sequences were designed using an older assembly version (hg18). In this release, the region on chromosome 5 was annotated with the gene ISCA1L. The three probes, however, also have a perfect match on chromosome 9 in the ISCA1 gene. In the new release (hg19), the ISCA1L gene was removed, i.e., the region on chromosome 5 is without annotation, and therefore Re-Annotator selected the region on chromosome 9 in the ISCA1 gene. Hence, it is important to keep the annotation tables of the probes up-to-date. ReMOAT, based on a genomic alignment, placed these probes in accordance with the Re-Annotator annotation (Fig 5). We recommend checking all given probe sequence annotations (second matches as well as other given genomic matches) also when using the ReMOAT annotation, as the given genomic location might be incorrect. Such an example is illustrated in Fig 6; the probe sequence was allocated to an intergenic region. We annotated this probe sequence to be on chromosome 17 within an exon of ABCA9, which was in accordance with the second match of the ReMOAT annotation.


Re-Annotator: Annotation Pipeline for Microarray Probe Sequences.

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

USCS genome browser graphic for the human ABCA9 gene.The gene is located on chromosome 9; the targeting Illumina probe is ILMN_1651396. Custom tracks represent the probe sequences annotated by (A) the Re-Annotator and (B) manufacturer and ReMOAT.
© Copyright Policy
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4591122&req=5

pone.0139516.g006: USCS genome browser graphic for the human ABCA9 gene.The gene is located on chromosome 9; the targeting Illumina probe is ILMN_1651396. Custom tracks represent the probe sequences annotated by (A) the Re-Annotator and (B) manufacturer and ReMOAT.
Mentions: A precise annotation of microarray probe sequences is essential for accurate biological findings and replicability. In this work, we present a pipeline to re-annotate probe sequences of gene expression microarrays using a custom-built mRNA reference and applied it to three Illumina BeadChip arrays (Human HT-12 v3, v4 and MouseRef-8 v2). The re-annotation revealed that indeed one quarter of the array probes were incompletely or incorrectly annotated by the manufacturer. A source of such mis-annotation may be due to changes in genome assembly or changes in exon/intron boundaries since the original design of the chip. Over 21% of re-annotated probes were assigned to different genes as given by the manufacturer. For example, three of the five Illumina HumanHT-12 v4 array probe sequences illustrated in Fig 5 all perfectly re-annotated within the first or second exon of the human gene ISCA1 on chromosome 9 using the Re-Annotator. Originally these probes were annotated on chromosome 5 within an intergenic region (Fig 5). A reason for this discrepancy was that the probe sequences were designed using an older assembly version (hg18). In this release, the region on chromosome 5 was annotated with the gene ISCA1L. The three probes, however, also have a perfect match on chromosome 9 in the ISCA1 gene. In the new release (hg19), the ISCA1L gene was removed, i.e., the region on chromosome 5 is without annotation, and therefore Re-Annotator selected the region on chromosome 9 in the ISCA1 gene. Hence, it is important to keep the annotation tables of the probes up-to-date. ReMOAT, based on a genomic alignment, placed these probes in accordance with the Re-Annotator annotation (Fig 5). We recommend checking all given probe sequence annotations (second matches as well as other given genomic matches) also when using the ReMOAT annotation, as the given genomic location might be incorrect. Such an example is illustrated in Fig 6; the probe sequence was allocated to an intergenic region. We annotated this probe sequence to be on chromosome 17 within an exon of ABCA9, which was in accordance with the second match of the ReMOAT annotation.

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.