Abstract
In this note, we describe an approach to the analysis of microarray data that uses significant biological information early in the process. By combining information about the biological function and chromosomal location of genes with microarray expression data, we are able to get a more comprehensive picture of the heterogeneity of different kinds of cancer. We also get information about the importance of different chromosomes and biological processes for distinguishing cancers. In general, methods that use existing biological knowledge are likely to provide more meaningful and more interpretable results than completely unsupervised methods.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genetics 25 (2000): 25–29. (See http://www.geneontology.org.)
National Cancer Institute. Cancer Genome Anatomy Project: Curated Cancer Gene Lists. http://cgap.nci.nih.gov/Genes/CuratedGeneLists (2001).
Nieves-Neira, W, Pommier Y. Apoptotic response to camptothecin and 7-hydroxystaurosporine (UCN-01) in the 8 human breast cancer cell lines of the NCI Anticancer Drug Screen: multifactorial relationships with topoisomerase I, protein kinase C, Bcl-2, p53, MDM-2 and caspase pathways. Int J Cancer 8 (1999): 396–404.
Ross, DT, Scherf, U, Eisen, MB, Perou, CM, Rees, C, Spellman, P, Iyer, V, Jeffrey, SS, Van de Rijn, M, Waltham, M, Pergamenschikov, A, Lee, JC, Lashkari, D, Shalon, D, Myers, TG, Weinstein, JN, Botstein, D, Brown, PO. Systematic variation in gene expression patterns in human cancer cell lines. Nature Genetics 24 (2000): 227–235.
Scherf, U, Ross, DT, Waltham, M, Smith, LH, Lee, JK, Tanabe, L, Kohn, KW, Reinhold, WC, Myers, TG, Andrews, DT, Scudiero, DA, Eisen, MB, Sausville, EA, Pommier, Y, Botstein, D, Brown, PO, Weinstein, JN. A gene expression database for the molecular pharmacology of cancer. Nature Genetics 24 (2000): 236–244.
Shi, Q, Chen, K, Li, L, Chang, JJ, Autry, C, Kozuka, M, Konoshima, T, Este, sJR, Lin, CM, Hamel, E. Antitumor agents, 154-Cytotoxic and antimitotic flavonols from Polanisia dodecandra. J Nat Prod 58 (1995): 475–482.
Virtaneva, K, Wright, FA, Tanner, SM, Yuan, B, Lemon, WJ, Caligiuri, MA, Bloomfield, CD, de La Chapelle, A, Krahe, R. Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics. Proc Natl Acad Sci USA 98 (2001): 1124–1129.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2002 Kluwer Academic Publishers
About this chapter
Cite this chapter
Coombes, K.R. et al. (2002). Biology-driven Clustering of Microarray Data. In: Lin, S.M., Johnson, K.F. (eds) Methods of Microarray Data Analysis II. Springer, Boston, MA. https://doi.org/10.1007/0-306-47598-7_5
Download citation
DOI: https://doi.org/10.1007/0-306-47598-7_5
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4020-7111-9
Online ISBN: 978-0-306-47598-6
eBook Packages: Springer Book Archive