APMA: DB and Tool for Quality Control, Mapping and Annotation of Human GeneChip Microarray Initial Probe Sequences

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The APMA website will be shutdown for maintenance from 9th May 2008 (Fri) 5pm to 12th May 2008 (Monday) 12pm. We apologize for the inconveniece caused.

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Affymetrix (GeneChip Human Genome U133 Plus 2.0 Array) Probesets Mapping and

Annotations Database (APMA)

One of the key problem facing microarray experiments is insufficient reliability of expression measurements due to sub-optimal probe design. APMA classifies GeneChip Human Genome initial target sequences based on specificity, complexity, and reliability to use in gene expression measurements. Discrepancies found in probeset annotation and target sequence mapping account for up to 30% of probesets, including about 25% of Affymetrix probesets derived from target sequences overlapped interspersed repeats and 1.8% of original target sequences with erroneous orientation of the sequences. 86% of U133 target sequences passed APMA software quality-control filtering. APMA provide design and visualization pipelines and DB for quality control of the initial probe sequences and analysis of U133 Plus 2 microarray measurements but can have general applicability to a variety of human gene expression profiling projects.

APMA Team:

Principal investigator: Vladimir Kuznetsov (2)
Software: Yuriy Orlov (1), Atif Shahab (1)
DB support and development: Kelvin Goh (2)

1 Genome Institute of Singapore, 60 Biopolis Street, Genome, 138672 Singapore
2 Bioinformatics Institute, 30 Biopolis Street, Matrix, 138671 Singapore

Contacts:

If you have any inquiries, contact us at affy@bii.a-star.edu.sg or vladimirk@bii.a-star.edu.sg

Relative Links

The NetAffx Analysis Center: http://www.affymetrix.com/analysis/index.affx
ADAPT: http://bioinformatics.picr.man.ac.uk/adapt/Welcome.adapt
MAP: http://xmap.picr.man.ac.uk/
AffyProbeMiner: http://discover.nci.nih.gov/affyprobeminer