Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics
Open accessAbstract
BACKGROUND: When processing microarray data sets, we recently noticed that some gene names were being changed inadvertently to non-gene names. RESULTS: A 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. CONCLUSIONS: Users 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.
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Spreadsheet software inadvertently converts gene symbols to dates and floating-point numbers, and these errors propagate downstream to annotation sets and other databases.
“It is a well-documented problem that spreadsheet software inadvertently converts gene symbols to dates and floating-point numbers, with these errors propagating downstream to annotation sets and other databases [1].”
From Gene name errors: Lessons not learned (2021) · cites this paper as [1]
The Results report that Excel converts gene names to dates and RIKEN identifiers to floating-point numbers. The Conclusions and Text say these errors have contaminated public databases, but the paper does not specifically identify annotation sets as a downstream destination. (LLM, conf=0.84)
Experimental — accuracy not yet measuredThe problem of Excel inadvertently converting gene symbols to dates and floating-point numbers was originally described in 2004.
“The problem of Excel software (Microsoft Corp., Redmond, WA, USA) inadvertently converting gene symbols to dates and floating-point numbers was originally described in 2004 [1].”
From Gene name errors are widespread in the scientific literature (2016) · cites this paper as [1]
Microsoft Excel, when used with default settings, converts gene names to dates and floating-point numbers.
“The spreadsheet software Microsoft Excel, when used with default settings, is known to convert gene names to dates and floating-point numbers.”
From Gene name errors are widespread in the scientific literature (2016) · cites this paper as [1]
When importing text files of transcriptome data into a spreadsheet program, gene symbols may be wrongly imported as dates, which can lead to erroneous conclusions about the affected genes.
“For example, when importing text files of transcriptome data into a spreadsheet program, gene symbols may be wrongly imported as dates (Zeeberg, 2004; Ziemann, 2016), which can lead to erroneous conclusions about the affected genes.”
From Guidance document on Good cell and tissue culture practice 2.0 (GCCP 2.0) (2021) · cites this paper as Zeeberg, 2004
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References 6 · Cited by 110
- Authors
- Zeeberg, B. R., Riss, J., Kane, D. W., Bussey, K. J., Uchio, E., Linehan, W. M., Barrett, J. C., & Weinstein, J. N.
- Affiliations
- National Institutes of Health (US)
- SRA International (United States) (US)
- Corresponding author
- Weinstein, John N
- Venue
- BMC Bioinformatics
- Published
- 2004-06-23
- Volume
- 5
- Issue
- 1
- Pages
- 80-80
- ISSN
- 1471-2105 (ISSN-L)
- PMC
- PMC459209
- OpenAlex
- W2171804472
- Cited by
- 110
- References
- 6
- Citations by year
- 2026: 2 · 2025: 8 · 2024: 2 · 2023: 6 · 2022: 8 · 2021: 10 · 2020: 7 · 2019: 9 · 2018: 7 · 2017: 11 · 2016: 5 · 2015: 4 · 2014: 3 · 2013: 1 · 2012: 3
- FWCI
- 1.54
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- BMC Bioinformatics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, other-oa)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- SRA International
- National Institutes of Health
- National Cancer Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- gene identifiers, Microsoft Excel, microarray data processing, data corruption
- MeSH terms
- Animals, Genes, Humans, Research Design, Software, Computational Biology, Oligonucleotide Array Sequence Analysis, Mice
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