ArticleBMC bioinformatics2004
Mistaken identifiers: gene name errors can be introduced inadvertently when using Excel in bioinformatics.
Article in BMC bioinformatics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
56 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic identification of mutations and copy number alterations associated with cancer patient prognosis.eLife · 2018Pooled it
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- Hotgenes: an R package for reducing bottlenecks in bulk omics data exploration and collaboration.Bioinformatics (Oxford, England) · 2026Article
- Rapid Exploratory Data Visualization for Cancer Genomics.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Protein-coding genes in humans and model mammals (mouse, rat and pig): gene identifiers and disambiguation of gene nomenclature retrieved from the Ensembl genome browser.BMC genomics · 2025Article
- Relational Databases for Behavior Science.Perspectives on behavior science · 2025Article
- Catalyzing computational biology research at an academic institute through an interest network.PLoS computational biology · 2025Article
- Guidelines for Research Data Integrity (GRDI).Scientific data · 2025Article
- The Venus score for the assessment of the quality and trustworthiness of biomedical datasets.BioData mining · 2025Article
- What is the real value of omics data? Enhancing research outcomes and securing long-term data excellence.Nucleic acids research · 2024Article
- Eleven quick tips for properly handling tabular data.PLoS computational biology · 2024Article
- The five pillars of computational reproducibility: bioinformatics and beyond.Briefings in bioinformatics · 2023Article
- Gene Updater: a web tool that autocorrects and updates for Excel misidentified gene names.Scientific reports · 2022Article
- Article
- Reproducible manuscript preparation with RMarkdown application to JMSACL and other Elsevier Journals.Journal of mass spectrometry and advances in the clinical lab · 2021Article
- Article
- Gene name errors: Lessons not learned.PLoS computational biology · 2021Article
- Sharing biological data: why, when, and how.FEBS letters · 2021Article
- iDEP Web Application for RNA-Seq Data Analysis.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Design and analysis of CRISPR-Cas experiments.Nature biotechnology · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
backgroundWhen processing microarray data sets, we recently noticed that some gene names were being changed inadvertently to non-gene names.
resultsA little detective work traced the problem to default date format conversions and floating-point format conversions in the very useful Excel program package. The date conversions affect at least 30 gene names; the floating-point conversions affect at least 2,000 if Riken identifiers are included. These conversions are irreversible; the original gene names cannot be recovered.
conclusionsUsers of Excel for analyses involving gene names should be aware of this problem, which can cause genes, including medically important ones, to be lost from view and which has contaminated even carefully curated public databases. We provide work-arounds and scripts for circumventing the problem.
Indexed as
Identifiers
What OpenQuestion holds
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.