ArticleNucleic acids research2002
Improving DNA array data quality by minimising 'neighbourhood' effects.
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 13 citations in OpenAlex.
- c-Myc and Rel/NF-kappaB are the two master transcriptional systems activated in the latency III program of Epstein-Barr virus-immortalized B cells.Journal of virology · 2009Article
- The majority of Escherichia coli mRNAs undergo post-transcriptional modification in exponentially growing cells.Nucleic acids research · 2006Article
- Prediction of mechanisms of action of antibacterial compounds by gene expression profiling.Antimicrobial agents and chemotherapy · 2004Article
- Panel of Bacillus subtilis reporter strains indicative of various modes of action.Antimicrobial agents and chemotherapy · 2004Article
- Feature extraction and signal processing for nylon DNA microarrays.BMC genomics · 2004Article
- Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling.Nucleic acids research · 2003Article
- Dose-dependent regulation of target gene expression and cell proliferation by c-Myc levels.TranscriptionArticle
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
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Abstract
Gene expression studies using cDNA arrays require robust and sensitive detection methods. Being extremely sensitive, radioactive detection suffers from the influence of signals positioned in each other's vicinity, the 'neighbourhood' effect. This limits the gene density of arrays and the quality of the results obtained. We have investigated the quantitative influence of different parameters on the 'neighbourhood' effect. By using a model experimental system, we could show that the effect is linear and depends only on the intensity of the hybridisation signal. We identified a common factor that can describe the influence of the neighbour spots based on their intensities. This factor is <1%, but it has to be taken into account if a high dynamic range of gene expression is to be detected. We could also derive the factor, although with less precision, from comparison of duplicate spots on arrays of 4565 different clones and replication of the hybridisation experiments. The calculated coefficient applied to our actual experimental results not only revealed previously undetected tissue or cell-specific expression differences, but also increased the dynamic range of detection. It thus provides a relatively simple way of improving DNA array data quality with few experimental modifications.
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