The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
Control Genes and Variability: Absence of Ubiquitous Reference Transcripts in Diverse Mammalian Expression Studies
Open accessAbstract
Control genes, commonly defined as genes that are ubiquitously expressed at stable levels in different biological contexts, have been used to standardize quantitative expression studies for more than 25 yr. We analyzed a group of large mammalian microarray datasets including the NCI60 cancer cell line panel, a leukemia tumor panel, and a phorbol ester induction time course as well as human and mouse tissue panels. Twelve housekeeping genes commonly used as controls in classical expression studies (including GAPD, ACTB, B2M, TUBA, G6PD, LDHA, and HPRT) show considerable variability of expression both within and across microarray datasets. Although we can identify genes with lower variability within individual datasets by heuristic filtering, such genes invariably show different expression levels when compared across other microarray datasets. We confirm these results with an analysis of variance in a controlled mouse dataset, showing the extent of variability in gene expression across tissues. The results show the problems inherent in the classical use of control genes in estimating gene expression levels in different mammalian cell contexts, and highlight the importance of controlled study design in the construction of microarray experiments. [Supplemental material available online at http://genome.mcgill.ca/∼pdlee/control_genes and and http://www.genome.org.]
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Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., Coller, H., Loh, M. L., Downing, J. R., Caligiuri, M. A., et al. (1999) · Science · doi:10.1126/science.286.5439.531 · Cited by 11,516
Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitareewan, S., Dmitrovsky, E., Lander, E. S., & Golub, T. R. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.6.2907 · Cited by 2,923
Housekeeping genes as internal standards: use and limits
Thellin, O., Zorzi, W., Lakaye, B., De Borman, B., Coumans, B., Hennen, G., Grisar, T., Igout, A., & Heinen, E. (1999) · Journal of Biotechnology · doi:10.1016/s0168-1656(99)00163-7 · Cited by 1,544
Control Selection for RNA Quantitation
Suzuki, T., Higgins, P. J., & Crawford, D. R. (2000) · BioTechniques · doi:10.2144/00292rv02 · Cited by 875
Butte, A. J., Tamayo, P., Slonim, D., Golub, T. R., & Kohane, I. S. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.220392197 · Cited by 605
Lander, E. S. (1999) · Nature Genetics · doi:10.1038/4427 · Cited by 554
WARRINGTON, J. A., NAIR, A., MAHADEVAPPA, M., & TSYGANSKAYA, M. (2000) · Physiological Genomics · doi:10.1152/physiolgenomics.2000.2.3.143 · Cited by 541
Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays.
Khan, J. I., Simon, R., Bittner, M. L., Chen, Y., Leighton, S. B., Pohida, T. J., Smith, P. D., Jiang, Y. Y., Gooden, G. C., Trent, J. M., et al. (1998) · PubMed · Cited by 437
Biomedical Discovery with DNA Arrays
Young, R. A. (2000) · Cell · doi:10.1016/s0092-8674(00)00005-2 · Cited by 352
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Cited by
Expósito-Rodríguez, M., Borges, A. A., Borges-Pérez, A., & Pérez, J. A. (2008) · BMC Plant Biology · doi:10.1186/1471-2229-8-131 · Cited by 787
Coexpression Analysis of Human Genes Across Many Microarray Data Sets
Lee, H. K., Hsu, A. K., Sajdak, J., Qin, J., & Pavlidis, P. (2004) · Genome Research · doi:10.1101/gr.1910904 · Cited by 770
Human housekeeping genes are compact
Eisenberg, E., & Levanon, E. Y. (2003) · Trends in Genetics · doi:10.1016/s0168-9525(03)00140-9 · Cited by 698
Lourenço, A. P., Mackert, A., dos Santos Cristino, A., & Simões, Z. L. P. (2008) · Apidologie · doi:10.1051/apido:2008015 · Cited by 355
Evaluation of candidate reference genes for qPCR in maize
Manoli, A., Sturaro, A., Trevisan, S., Quaggiotti, S., & Nonis, A. (2012) · Journal of Plant Physiology · doi:10.1016/j.jplph.2012.01.019 · Cited by 274
Metadata
- Authors
- Lee, P. D., Sladek, R., Greenwood, C. M. T., & Hudson, T. J.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2002-02-01
- Volume
- 12
- Issue
- 2
- Pages
- 292-297
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W2135598172
- Cited by
- 369
- References
- 15
- Type
- posted content
- Language
- en
- Open access
- bronze
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- Lee, P. D., Sladek, R., Greenwood, C. M. T., & Hudson, T. J. (2002). Control Genes and Variability: Absence of Ubiquitous Reference Transcripts in Diverse Mammalian Expression Studies. Genome Research. https://doi.org/10.1101/gr.217802
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