Summary
Several statistical tests have been introduced for the comparison of serial analysis of gene expression (SAGE) libraries to quantitatively analyze the differential expression of genes. As each SAGE library is only one measurement, the necessary information on biological variation or experimental precision is lacking. Therefore, each test includes its own approach to derive such a variance measure from the data set or a theoretical distribution. Because the confidence in tag counts depends on the library size, a test between two or more libraries should be based on original tag counts. When groups of libraries are compared, the test should determine that the proportion of a specific tag in all libraries is the same (null hypothesis), but also offer the possibility to detect specific differences between individual libraries and groups of libraries. The Z-test and the G-test encompass these characteristics and are described for the comparison of two libraries and (two or more) groups of libraries, respectively.
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Reference
Stollberg, J., Urschitz, J., Urban, Z., and Boyd, C. D. (2000) A quantitative evaluation of SAGE. Genome Res. 10, 1241–1248.
Ruijter, J. M., Van Kampen, A. H., and Baas, F. (2002) Statistical evaluation of SAGE libraries: consequences for experimental design. Physiol. Genomics 11, 37–44.
Kal, A. J., van Zonneveld, A. J., Benes, V., et al. (1999) Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources. Mol. Biol. Cell 10, 1859–1872.
Schaaf, G. J., Ruijter, J. M., van Ruissen, F., et al. (2005) Full transcriptome analysis of rhabdomyosarcoma, normal, and fetal skeletal muscle: statistical comparison of multiple SAGE libraries. FASEB J. 19, 404–406.
Altman, D. (1991) Practical Statistics for Medical Research. Chapman-Hall, London: pp. 161–167, 253–258.
Man, M. Z., Wang, X., and Wang, Y. (2000) POWER_SAGE: comparing statistical tests for SAGE experiments. Bioinformatics 16, 953–959.
Audic, S. and Claverie, J. M. (1997) The significance of digital gene expression profiles. Genome Res. 7, 986–995.
Ryu, B., Jones, J., Blades, N. J., et al. (2002) Relationships and differentially expressed genes among pancreatic cancers examined by large-scale serial analysis of gene expression. Cancer Res. 62, 819–826.
Walter-Yohrling, J., Cao, X., Callahan, M., et al. (2003) Identification of genes expressed in malignant cells that promote invasion. Cancer Res. 63, 8939–8947.
Baggerly, K. A., Deng, L., Morris, J. S., and Aldaz, C. M. (2003) Differential expression in SAGE: accounting for normal between-library variation. Bioinformatics 19, 1477–1483.
Baggerly, K. A., Deng, L., Morris, J. S., and Aldaz, C. M. (2004) Overdispersed logistic regression for SAGE: modelling multiple groups and covariates. BMC Bioinformatics 5, 144.
Lu, J., Tomfohr, J. K., and Kepler, T. B. (2005) Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach. BMC Bioinformatics 6, 165.
Michiels, E. M., Oussoren, E., Van Groenigen, M., et al. (1999) Genes differentially expressed in medulloblastoma and fetal brain. Physiol. Genomics 1, 83–91.
Sokal, R. R. and Rohlf, F. J. (1995) Analysis of frequencies, in Biometry, the Principles and Practice of Statistics in Biological Research, 3rd edition. W. H. Freeman and Co.: New York: pp. 685–789.
Hochberg, Y. and Benjamini, Y. (1990) More powerful procedures for multiple significance testing. Stat. Med. 9, 811–818.
van den Oord, E. J. and Sullivan, P. F. (2003) False discoveries and models for gene discovery. Trends Genet. 19, 537–542.
Shannon, W., Culverhouse, R., and Duncan, J. (2003) Analyzing microarray data using cluster analysis. Pharmacogenomics 4, 41–52.
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Schaaf, G.J., van Ruissen, F., van Kampen, A., Kool, M., Ruijter, J.M. (2008). Statistical Comparison of Two or More SAGE Libraries. In: Nielsen, K.L. (eds) Serial Analysis of Gene Expression (SAGE). Methods in Molecular Biology™, vol 387. Humana Press. https://doi.org/10.1007/978-1-59745-454-4_12
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DOI: https://doi.org/10.1007/978-1-59745-454-4_12
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