ArticleNucleic acids research2007
Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
32 citing papers in PubMed, 83 citations in OpenAlex.
- Deciphering transcriptomic changes in chemobrain: a comprehensive review.Acta neuropathologica communications · 2025Review
- Machine learning aided construction of the quorum sensing communication network for human gut microbiota.Nature communications · 2022Article
- Transcriptomic analysis of saffron at different flowering stages using RNA sequencing uncovers cytochrome P450 genes involved in crocin biosynthesis.Molecular biology reports · 2021Article
- Processing and Analysis of RNA-seq Data from Public Resources.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Transcriptomic biomarkers for predicting response to neoadjuvant treatment in oesophageal cancer.Gastroenterology report · 2020Review
- Adipogenesis, Osteogenesis, and Chondrogenesis of Human Mesenchymal Stem/Stromal Cells: A Comparative Transcriptome Approach.Frontiers in cell and developmental biology · 2020Review
- Omics Analysis for Dinoflagellates Biology Research.Microorganisms · 2019Review
- Targeted expression profiling by RNA-Seq improves detection of cellular dynamics during pregnancy and identifies a role for T cells in term parturition.Scientific reports · 2019Article
- Uncovering the Transcriptional Correlates of Hub Connectivity in Neural Networks.Frontiers in neural circuits · 2019Review
- Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing.BMC genomics · 2017Article
- Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity.Molecular psychiatry · 2017Article
- A Pipeline for High-Throughput Concentration Response Modeling of Gene Expression for Toxicogenomics.Frontiers in genetics · 2017Article
- Comprehensive evaluation of AmpliSeq transcriptome, a novel targeted whole transcriptome RNA sequencing methodology for global gene expression analysis.BMC genomics · 2015Article
- Plant transcriptomics and responses to environmental stress: an overview.Journal of genetics · 2015Review
- Isoform-level brain expression profiling of the spermidine/spermine N1-Acetyltransferase1 (SAT1) gene in major depression and suicide.Neurobiology of disease · 2015Article
- Comparative Analysis of Anther Transcriptome Profiles of Two Different Rice Male Sterile Lines Genotypes under Cold Stress.International journal of molecular sciences · 2015Article
- Transcriptome Profiles of Human Lung Epithelial Cells A549 Interacting with Aspergillus fumigatus by RNA-Seq.PloS one · 2015Article
- PDEGEM: Modeling non-uniform read distribution in RNA-Seq data.BMC medical genomics · 2015Article
- Advanced Applications of RNA Sequencing and Challenges.Bioinformatics and biology insights · 2015Review
- Single-cell analysis of the transcriptome and its application in the characterization of stem cells and early embryos.Cellular and molecular life sciences : CMLS · 2014Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
A generic DNA microarray design applicable to any species would greatly benefit comparative genomics. We have addressed the feasibility of such a design by leveraging the great feature densities and relatively unbiased nature of genomic tiling microarrays. Specifically, we first divided each Homo sapiens Refseq-derived gene's spliced nucleotide sequence into all of its possible contiguous 25 nt subsequences. For each of these 25 nt subsequences, we searched a recent human transcript mapping experiment's probe design for the 25 nt probe sequence having the fewest mismatches with the subsequence, but that did not match the subsequence exactly. Signal intensities measured with each gene's nearest-neighbor features were subsequently averaged to predict their gene expression levels in each of the experiment's thirty-three hybridizations. We examined the fidelity of this approach in terms of both sensitivity and specificity for detecting actively transcribed genes, for transcriptional consistency between exons of the same gene, and for reproducibility between tiling array designs. Taken together, our results provide proof-of-principle for probing nucleic acid targets with off-target, nearest-neighbor features.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.