The LO-BaFL method and ALS microarray expression analysis.

Background: Sporadic Amyotrophic Lateral Sclerosis (sALS) is a devastating, complex disease of unknown etiology. We studied this disease with microarray technology to capture as much biological complexity as possible. The Affymetrix-focused BaFL pipeline takes into account problems with probes that arise from physical and biological properties, so we adapted it to handle the long-oligonucleotide probes on our arrays (hence LO-BaFL).

ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs.

Background: Probes on a microarray represent a frozen view of a genome and are quickly outdated when new sequencing studies extend our knowledge, resulting in significant measurement error when analyzing any microarray experiment. There are several bioinformatics approaches to improve probe assignments, but without in-house programming expertise, standardizing these custom array specifications as a usable file (e.g.

Application of equilibrium models of solution hybridization to microarray design and analysis.

Background: The probe percent bound value, calculated using multi-state equilibrium models of solution hybridization, is shown to be useful in understanding the hybridization behavior of microarray probes having 50 nucleotides, with and without mismatches. These longer oligonucleotides are in widespread use on microarrays, but there are few controlled studies of their interactions with mismatched targets compared to 25-mer based platforms.

Principal Findings: 50-mer oligonucleotides with centrally placed single, double and triple mismatches were spotted on an array.

A white-box approach to microarray probe response characterization: the BaFL pipeline.

Background: Microarrays depend on appropriate probe design to deliver the promise of accurate genome-wide measurement. Probe design, ideally, produces a unique probe-target match with homogeneous duplex stability over the complete set of probes. Much of microarray pre-processing is concerned with adjusting for non-ideal probes that do not report target concentration accurately.

AffyMAPSDetector: a software tool to characterize Affymetrix GeneChip expression arrays with respect to SNPs.

Background: Affymetrix gene expression arrays incorporate paired perfect match (PM) and mismatch (MM) probes to distinguish true signals from those arising from cross-hybridization events. A MM signal often shows greater intensity than a PM signal; we propose that one underlying cause is the presence of allelic variants arising from single nucleotide polymorphisms (SNPs). To annotate and characterize SNP contributions to anomalous probe binding behavior we have developed a software tool called AffyMAPSDetector.

Secondary structure in the target as a confounding factor in synthetic oligomer microarray design.

Background: Secondary structure in the target is a property not usually considered in software applications for design of optimal custom oligonucleotide probes. It is frequently assumed that eliminating self-complementarity, or screening for secondary structure in the probe, is sufficient to avoid interference with hybridization by stable secondary structures in the probe binding site. Prediction and thermodynamic analysis of secondary structure formation in a genome-wide set of transcripts from Brucella suis 1330 demonstrates that the properties of the target molecule have the potential to strongly influence the rate and extent of hybridization between transcript and tethered oligonucleotide probe in a microarray experiment.

ESTAP--an automated system for the analysis of EST data.

The EST Analysis Pipeline (ESTAP) is a set of analytical procedures that automatically verify, cleanse, store and analyze ESTs generated on high-throughput platforms. It uses a relational database to store sequence data and analysis results, which facilitates both the search for specific information and statistical analysis. ESTAP provides for easy viewing of the original and cleansed data, as well as the analysis results via a Web browser.