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and genotyping analysis.However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases.It is primarily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 However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases.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


Annotation pipeline.Schematic overview of the computational pipeline flow: (top) creating the in silico mRNA reference database and (bottom) step-wise alignment process. Purple sequences in the left column correspond to alignments to the in silico reference and brown sequences in the right column correspond to alignments to the genome.
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pone.0139516.g001: Annotation pipeline.Schematic overview of the computational pipeline flow: (top) creating the in silico mRNA reference database and (bottom) step-wise alignment process. Purple sequences in the left column correspond to alignments to the in silico reference and brown sequences in the right column correspond to alignments to the genome.

Mentions: First, for each transcript in the RefSeq database the genomic location of the exons are extracted. Next, the genomic sequence of the exons of each isoform are concatenated to form one in silico mRNA. These sequences (one per listed isoform in the database) form the reference database for the mapping step (Fig 1).


Re-Annotator: Annotation Pipeline for Microarray Probe Sequences.

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

Annotation pipeline.Schematic overview of the computational pipeline flow: (top) creating the in silico mRNA reference database and (bottom) step-wise alignment process. Purple sequences in the left column correspond to alignments to the in silico reference and brown sequences in the right column correspond to alignments to the genome.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139516.g001: Annotation pipeline.Schematic overview of the computational pipeline flow: (top) creating the in silico mRNA reference database and (bottom) step-wise alignment process. Purple sequences in the left column correspond to alignments to the in silico reference and brown sequences in the right column correspond to alignments to the genome.
Mentions: First, for each transcript in the RefSeq database the genomic location of the exons are extracted. Next, the genomic sequence of the exons of each isoform are concatenated to form one in silico mRNA. These sequences (one per listed isoform in the database) form the reference database for the mapping step (Fig 1).

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.