ArticleBMC bioinformatics2011
Jetset: selecting the optimal microarray probe set to represent a gene.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 207 papers, 6 of them syntheses that pooled it.
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Who cites it
207 citing papers in PubMed, 6 syntheses or guidelines pooled it.
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- Mitochondrial Acetyl-CoA Synthetase 3 is Biosignature of Gastric Cancer Progression.Cancer medicine · 2018Pooled it
- The association between copper transporters and the prognosis of cancer patients undergoing chemotherapy: a meta-analysis of literatures and datasets.Oncotarget · 2017Pooled it
- Meta-analysis of organ-specific differences in the structure of the immune infiltrate in major malignancies.Oncotarget · 2015Pooled it
- Systematic review of genome-wide gene expression studies of bipolar disorder.BMC psychiatry · 2013Pooled it
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- Integrative Bioinformatic Characterization of the HDAC6-Driven Cytoskeleton-Wnt Signaling Interface in Hepatocellular Carcinoma: Implications for Immune Modulation and Therapeutic Targeting.International journal of molecular sciences · 2026Article
- PRSS23 promotes ovarian cancer peritoneal dissemination independent of protease activity.The Journal of biological chemistry · 2026Article
- Discordance between IHC/FISH and RNA expression-based assessment of ER/HER2 status, and its prognostic impact assessed by propensity score matching.BMC cancer · 2026Article
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- High-throughput Genome Wide CRISPR Knock Out mechanical sort identifies genes driving metastatic cancer cell softening.bioRxiv : the preprint server for biology · 2026Article
- MRCKα represses GEF-H1 mediated RhoA activation to promote ovarian cancer spheroid growth and invasion.bioRxiv : the preprint server for biology · 2026Article
- ColoStem, a core oncofetal signature that identifies poor prognosis colorectal tumors.British journal of cancer · 2026Article
- The Emerging Role of FAM171A2 in Gynecological Malignancies: Bioinformatic Insights from UCEC and Ovarian Cancer.International journal of molecular sciences · 2025Article
- Disrupting tRNA modifications to target mitochondrial vulnerabilities in drug-resistant leukemia cells.Blood · 2025Article
- HERC2 as a Potential Biomarker for Prognosis and Response to Bevacizumab in Ovarian Cancer: A Bioinformatics Approach.Reproductive sciences (Thousand Oaks, Calif.) · 2025Article
147 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
backgroundInterpretation of gene expression microarrays requires a mapping from probe set to gene. On many Affymetrix gene expression microarrays, a given gene may be detected by multiple probe sets, which may deliver inconsistent or even contradictory measurements. Therefore, obtaining an unambiguous expression estimate of a pre-specified gene can be a nontrivial but essential task.
resultsWe developed scoring methods to assess each probe set for specificity, splice isoform coverage, and robustness against transcript degradation. We used these scores to select a single representative probe set for each gene, thus creating a simple one-to-one mapping between gene and probe set. To test this method, we evaluated concordance between protein measurements and gene expression values, and between sets of genes whose expression is known to be correlated. For both test cases, we identified genes that were nominally detected by multiple probe sets, and we found that the probe set chosen by our method showed stronger concordance.
conclusionsThis method provides a simple, unambiguous mapping to allow assessment of the expression levels of specific genes of interest.
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