The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
GATHER: a systems approach to interpreting genomic signatures
Open accessAbstract
Motivation: Understanding the full meaning of the biology captured in molecular profiles, within the context of the entire biological system, cannot be achieved with a simple examination of the individual genes in the signature. To facilitate such an understanding, we have developed GATHER, a tool that integrates various forms of available data to elucidate biological context within molecular signatures produced from high-throughput post-genomic assays. Results: Analyzing the Rb/E2F tumor suppressor pathway, we show that GATHER identifies critical features of the pathway. We further show that GATHER identifies common biology in a series of otherwise unrelated gene expression signatures that each predict breast cancer outcome. We quantify the performance of GATHER and find that it successfully predicts 90% of the functions over a broad range of gene groups. We believe that GATHER provides an essential tool for extracting the full value from molecular signatures generated from genome-scale analyses. Availability: GATHER is available at Contact: j.nevins@duke.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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Gene expression profiling predicts clinical outcome of breast cancer
van 't Veer, L. J., Dai, H., van de Vijver, M. J., He, Y. D., Hart, A. A. M., Mao, M., Peterse, H. L., van der Kooy, K., Marton, M. J., Witteveen, A. T., et al. (2002) · Nature · doi:10.1038/415530a · Cited by 9,536
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Use of proteomic patterns in serum to identify ovarian cancer
Petricoin, E. F., Ardekani, A. M., Hitt, B. A., Levine, P. J., Fusaro, V. A., Steinberg, S. M., Mills, G. B., Simone, C., Fishman, D. A., Kohn, E. C., et al. (2002) · The Lancet · doi:10.1016/s0140-6736(02)07746-2 · Cited by 3,236
Microarray data analysis: from disarray to consolidation and consensus
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E2F integrates cell cycle progression with DNA repair, replication, and G 2 /M checkpoints
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Cited by
Peng, J., Hamanishi, J., Matsumura, N., Abiko, K., Murat, K., Baba, T., Yamaguchi, K., Horikawa, N., Hosoe, Y., Murphy, S. K., et al. (2015) · Cancer Research · doi:10.1158/0008-5472.can-14-3098 · Cited by 525
Zheng, B., Ren, T., Huang, Y., Sun, K., Wang, S., Bao, X., Liu, K., & Guo, W. (2018) · Journal of Hematology & Oncology · doi:10.1186/s13045-018-0560-1 · Cited by 151
A comprehensive joint analysis of the long and short RNA transcriptomes of human erythrocytes.
Doss, J. F., Corcoran, D. L., Jima, D. D., Telen, M. J., Dave, S. S., & Chi, J.-T. (2015) · BMC Genomics · doi:10.1186/s12864-015-2156-2 · Cited by 113
Schlereth, K., Heyl, C., Krampitz, A.-M., Mernberger, M., Finkernagel, F., Scharfe, M., Jarek, M., Leich, E., Rosenwald, A., & Stiewe, T. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003726 · Cited by 87
Varma, S., Cao, Y., Tagne, J.-B., Lakshminarayanan, M., Li, J., Friedman, T. B., Morell, R. J., Warburton, D., Kotton, D. N., & Ramirez, M. I. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.408401 · Cited by 79
Metadata
- Authors
- Chang, J. T., & Nevins, J. R.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-06-29
- Volume
- 22
- Issue
- 23
- Pages
- 2926-2933
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2114381883
- Cited by
- 321
- References
- 9
- FWCI
- 3.81
- Type
- journal article
- Language
- en
- Open access
- bronze
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