Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper – Excel-based tool using pair-wise correlations

Pfaffl, Michael W.; Tichopad, Ales; Prgomet, Christian; Neuvians, Tanja P.

doi:10.1023/b:bile.0000019559.84305.47

Cited by 5,065Molecular Biology Techniques and ApplicationsGene expression and cancer classificationRNA Research and Splicing

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Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper – Excel-based tool using pair-wise correlations

Pfaffl, Michael W., Tichopad, Ales, Prgomet, Christian, Neuvians, Tanja P.·2004·Biotechnology Letters

DOI 10.1023/b:bile.0000019559.84305.47

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Abstract

The stability of standard gene expression is an elementary prerequisite for internal standardisation of target gene expression data and many so called housekeeping genes with assumed stable expression can exhibit either up- or down-regulation under some experimental conditions. The developed, and herein presented, software called BestKeeper determines the best suited standards, out of ten candidates, and combines them into an index. The index can be compared with further ten target genes to decide, whether they are differentially expressed under an applied treatment. All data processing is based on crossing points. The BestKeeper software tool was validated on four housekeeping genes and 10 members of the somatotropic axis differentially expressed in bovine corpora lutea total RNA. The BestKeeper application and necessary information about data processing and handling can be downloaded on http://www.wzw.tum.de/gene-quantification/bestkeeper.html.

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BestKeeper software was used to search for stable reference genes among all genes tested.
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Authors: Pfaffl, M. W., Tichopad, A., Prgomet, C., & Neuvians, T. P.
Affiliations: Technical University of Munich (DE)
ORCID: Pfaffl, Michael W.
Venue: Biotechnology Letters
Publisher: Springer Science and Business Media LLC
Published: 2004-03
Volume: 26
Issue: 6
Pages: 509-515
ISSN: 0141-5492 (ISSN-L)
1573-6776
DOI: 10.1023/b:bile.0000019559.84305.47
OpenAlex: W2099824652
Cited by: 5,065
References: 19
Citations by year: 2026: 180 · 2025: 273 · 2024: 289 · 2023: 287 · 2022: 311 · 2021: 369 · 2020: 391 · 2019: 379 · 2018: 372 · 2017: 333 · 2016: 321 · 2015: 326 · 2014: 282 · 2013: 223 · 2012: 188
FWCI: 14.92
Type: journal article
Language: en
Open access: closed
Licence: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
Locations: Biotechnology Letters (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Keywords: housekeeping genes, gene expression stability, two-particle correlations, differentially expressed genes, sample integrity, crossing points, somatotropic axis, bovine corpus luteum, gene expression analysis
MeSH terms: Animals, Cattle, Corpus Luteum, Female, Genes, RNA, Software, Gene Expression, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling

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Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper – Excel-based tool using pair-wise correlations

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