ArticleNucleic acids research2004
Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed, 185 citations in OpenAlex.
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- High-Efficiency Reverse (5'→3') Synthesis of Complex DNA Microarrays.Scientific reports · 2018Article
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- Influence of Glucose Availability and CRP Acetylation on the Genome-Wide Transcriptional Response ofFrontiers in microbiology · 2018Article
- The effect of insecticide synergist treatment on genome-wide gene expression in a polyphagous pest.Scientific reports · 2017Article
- Entrainment of Breast Cell Lines Results in Rhythmic Fluctuations of MicroRNAs.International journal of molecular sciences · 2017Article
- Simultaneous Detection of Nine Key Bacterial Respiratory Pathogens Using Luminex xTAGInternational journal of environmental research and public health · 2017Article
- Simultaneous genome-wide gene expression and transcript isoform profiling in the human malaria parasite.PloS one · 2017Article
- Highly specific SNP detection using 2D graphene electronics and DNA strand displacement.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Simultaneous Detection of Five Pathogens from Cerebrospinal Fluid Specimens Using Luminex Technology.International journal of environmental research and public health · 2016Article
- Sexual Dimorphism and Aging in the Human Hyppocampus: Identification, Validation, and Impact of Differentially Expressed Genes by Factorial Microarray and Network Analysis.Frontiers in aging neuroscience · 2016Article
13 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene-specific oligonucleotide probes are currently used in microarrays to avoid cross-hybridization of highly similar sequences. We developed an approach to determine the optimal number and length of gene-specific probes for accurate transcriptional profiling studies. The study surveyed probe lengths from 25 to 1000 nt. Long probes yield better signal intensity than short probes. The signal intensity of short probes can be improved by addition of spacers or using higher probe concentration for spotting. We also found that accurate gene expression measurement can be achieved with multiple probes per gene and fewer probes are needed if longer probes rather than shorter probes are used. Based on theoretical considerations that were confirmed experimentally, our results showed that 150mer is the optimal probe length for expression measurement. Gene-specific probes can be identified using a computational approach for 150mer probes and they can be treated like long cDNA probes in terms of the hybridization reaction for high sensitivity detection. Our experimental data also show that probes which do not generate good signal intensity give erroneous expression ratio measurement results. To use microarray probes without experimental validation, gene-specific probes approximately 150mer in length are necessary. However, shorter oligonucleotide probes also work well in gene expression analysis if the probes are validated by experimental selection or if multiple probes per gene are used for expression measurement.
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