The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Significance analysis of time course microarray experiments
Open accessAbstract
Characterizing the genome-wide dynamic regulation of gene expression is important and will be of much interest in the future. However, there is currently no established method for identifying differentially expressed genes in a time course study. Here we propose a significance method for analyzing time course microarray studies that can be applied to the typical types of comparisons and sampling schemes. This method is applied to two studies on humans. In one study, genes are identified that show differential expression over time in response to in vivo endotoxin administration. By using our method, 7,409 genes are called significant at a 1% false-discovery rate level, whereas several existing approaches fail to identify any genes. In another study, 417 genes are identified at a 10% false-discovery rate level that show expression changing with age in the kidney cortex. Here it is also shown that as many as 47% of the genes change with age in a manner more complex than simple exponential growth or decay. The methodology proposed here has been implemented in the freely distributed and open-source edge software package.
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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
A network-based analysis of systemic inflammation in humans
Program, I. A. H. R. T. I. L. S. C. R., Calvano, S. E., Xiao, W., Richards, D. R., Felciano, R. M., Baker, H. V., Cho, R. J., Chen, R. O., Brownstein, B. H., Cobb, J. P., et al. (2005) · Nature · doi:10.1038/nature03985 · Cited by 1,429
Self-citationA Transcriptional Profile of Aging in the Human Kidney
Rodwell, G. E. J., Sonu, R., Zahn, J. M., Lund, J., Wilhelmy, J., Wang, L., Xiao, W., Mindrinos, M., Crane, E., Segal, E., et al. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020427 · Cited by 338
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MEME SUITE: tools for motif discovery and searching
Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J., Li, W. W., & Noble, W. S. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp335 · Cited by 10,648
Genomic responses in mouse models poorly mimic human inflammatory diseases
Seok, J., Warren, H. S., Cuenca, A. G., Mindrinos, M. N., Baker, H. V., Xu, W., Richards, D. R., McDonald-Smith, G. P., Gao, H., Hennessy, L., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1222878110 · Cited by 3,005
Self-citationCapturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis
Leek, J. T., & Storey, J. D. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030161 · Cited by 1,930
Self-citationInduction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1
Wu, C., Yosef, N., Thalhamer, T., Zhu, C., Xiao, S., Kishi, Y., Regev, A., & Kuchroo, V. K. (2013) · Nature · doi:10.1038/nature11984 · Cited by 1,022
Dynamic regulatory network controlling TH17 cell differentiation
Yosef, N., Shalek, A. K., Gaublomme, J. T., Jin, H., Lee, Y., Awasthi, A., Wu, C., Karwacz, K., Xiao, S., Jorgolli, M., et al. (2013) · Nature · doi:10.1038/nature11981 · Cited by 682
Metadata
- Authors
- Storey, J. D., Xiao, W., Leek, J. T., Tompkins, R. G., & Davis, R. W.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2005-09-02
- Volume
- 102
- Issue
- 36
- Pages
- 12837-12842
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2149566602
- Cited by
- 567
- References
- 3
- FWCI
- 14.29
- Type
- journal article
- Language
- en
- Open access
- green
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