The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Assessing Gene Significance from cDNA Microarray Expression Data via Mixed Models
Open accessAbstract
The determination of a list of differentially expressed genes is a basic objective in many cDNA microarray experiments. We present a statistical approach that allows direct control over the percentage of false positives in such a list and, under certain reasonable assumptions, improves on existing methods with respect to the percentage of false negatives. The method accommodates a wide variety of experimental designs and can simultaneously assess significant differences between multiple types of biological samples. Two interconnected mixed linear models are central to the method and provide a flexible means to properly account for variability both across and within genes. The mixed model also provides a convenient framework for evaluating the statistical power of any particular experimental design and thus enables a researcher to a priori select an appropriate number of replicates. We also suggest some basic graphics for visualizing lists of significant genes. Analyses of published experiments studying human cancer and yeast cells illustrate the results.
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Cites
Cluster analysis and display of genome-wide expression patterns
Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14863 · Cited by 16,184
Power Calculations for General Linear Multivariate Models Including Repeated Measures Applications
Muller, K. E., Lavange, L. M., Ramey, S. L., & Ramey, C. T. (1992) · Journal of the American Statistical Association · doi:10.1080/01621459.1992.10476281 · Cited by 230
Cited by
Smyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1027 · Cited by 11,829
Aït Yahya-Graison, E., Aubert, J., Dauphinot, L., Rivals, I., Prieur, M., Golfier, G., Rossier, J., Personnaz, L., Créau, N., Bléhaut, H., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/520000 · Cited by 338
Sartor, M. A., Tomlinson, C. R., Wesselkamper, S. C., Sivaganesan, S., Leikauf, G. D., & Medvedovic, M. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-538 · Cited by 263
Geographical genomics of human leukocyte gene expression variation in southern Morocco
Idaghdour, Y., Czika, W., Shianna, K. V., Lee, S. H., Visscher, P. M., Martin, H. C., Miclaus, K., Jadallah, S. J., Goldstein, D. B., Wolfinger, R. D., et al. (2010) · Nature Genetics · doi:10.1038/ng.495 · Cited by 151
Self-citationSmeianov, V. V., Wechter, P., Broadbent, J. R., Hughes, J. E., Rodríguez, B. T., Christensen, T. K., Ardö, Y., & Steele, J. L. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00005-07 · Cited by 97
Metadata
- Authors
- Wolfinger, R. D., Gibson, G., Wolfinger, E. D., Bennett, L., Hamadeh, H., Bushel, P., Afshari, C., & Paules, R. S.
- Venue
- Journal of Computational Biology
- Publisher
- SAGE Publications
- Published
- 2001-11
- Volume
- 8
- Issue
- 6
- Pages
- 625-637
- ISSN
- 1066-5277 (ISSN-L)
- 1557-8666
- OpenAlex
- W2002810210
- Cited by
- 1,117
- References
- 2
- FWCI
- 26.71
- Type
- journal article
- Language
- en
- Open access
- green
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- Wolfinger, R. D., Gibson, G., Wolfinger, E. D., Bennett, L., Hamadeh, H., Bushel, P., Afshari, C., & Paules, R. S. (2001). Assessing Gene Significance from cDNA Microarray Expression Data via Mixed Models. Journal of Computational Biology. https://doi.org/10.1089/106652701753307520
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