XHM: A system for detection of potential cross hybridizations in DNA microarrays

Kristian Flikka,Astrid Laegreid,Fekadu Yadetie,Inge Jonassen

doi:10.1186/1471-2105-5-117

Abstract

BackgroundMicroarrays have emerged as the preferred platform for high throughput gene expression analysis. Cross-hybridization among genes with high sequence similarities can be a source of error reducing the reliability of DNA microarray results.ResultsWe have developed a tool called XHM (cross hybridization on microarrays) for assessment of the reliability of hybridization signals by detecting potential cross-hybridizations on DNA microarrays. This is done by comparing the sequences of the probes against an extensive database representing the transcriptome of the organism in question. XHM is available online at .ConclusionsUsing XHM with its user-adjustable parameters will enable scientists to check their lists of differentially expressed genes from microarray experiments for potential cross-hybridizations. This provides information that may be useful in the validation of the microarray results.

Highlights

Microarrays have emerged as the preferred platform for high throughput gene expression analysis
In the final section we report some example results using our system on three cDNA probe sets for human, mouse and rat, and one oligonucleotide probe set for mouse
For the mouse clone set it appears that the BeGIn database is the best choice, and for the human clone set it seems that RefSeq or UniGene Unique may be two good choices

Summary

Introduction

Microarrays have emerged as the preferred platform for high throughput gene expression analysis. One of the major concerns of cDNA microarrays is crosshybridization of the labeled RNA (or cDNA) to non-target homologous probe sequences on the array [4,5]. Crosshybridizations that may arise due to poly(A)-tail of mRNA or repetitive elements may be reduced or eliminated using hybridization blocking reagents like poly(A) oligonucleotides [6] or Cot DNA. Another major source of crosshybridization may come from conserved sequences shared by two or more cDNAs, such as gene family members [4,7]. Analysis of sequenced multicellular eukaryotic genomes suggests that a large percentage of genes belong to gene families, some of which have high sequence (page number not for citation purposes)

Results

Discussion

Conclusion