Reading list for microarrays

Biological Background

L Gonick, M Wheelis. The Cartoon Guide to Genetics. New York: Harper Perennial, 1991.

HF Lodish et al. Molecular Cell Biology. New York: WH Freeman, 2000.

WK Purves. Life, the science of biology. New York: WH Freeman, 2001.

A short background from a statistician’s perspective can be found in Technical Report 576 (http://www.stat.berkeley.edu/tech-reports/index.html)

A quick introduction to elements of biology – cells, molecules, genes, functional genomics, microarrays (by A Brazma, EMBL – European Bioinformatics Institute) http://industry.ebi.ac.uk/~brazma/Biointro/biology.html

The Chipping Forecast, Supplement to Nature Genetics v.21 (January 1999). This is a special issue on microarrays.

A web animation of cDNA microarray methodology can be viewed at http://www.bio.davidson.edu/courses/genomics/chip/chip.html

Example Studies

Some of the most cited studies are listed here; several have publicly available data.

Caveat: these studies vary in quality of data analysis; inclusion here is not necessarily an endorsement of the methods used!

AA Alizadeh, MB Eisen, RE Davis, C Ma, IS Lossos, A Rosenwald, JC Boldrick, H Sabet, T Tran, X Yu, JI Powell, L Yang, GE Marti, T Moore, J Hudson Jr, L Lu, DB Lewis, R Tibshirani, G Sherlock, WC Chan, TC Greiner, DD Weisenburger, JO Armitage, R Warnke, R Levy, W Wilson, MR Grever, JC Byrd, D Botstein, PO Brown, LM Staudt. Different types of diffuse large b-cell lymphoma identified by gene expression profiling. Nature, 403:503-511, 2000.

U Alon, N Barkai, DA Notterman, K Gish, S Ybarra, D Mack, AJ Levine. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci, 96:6745-6750, 1999.

M Bittner, P Meltzer, Y Chen, Y Jiang, E Seftor, M Hendrix, M Radmacher, R Simon, Z Yakhini, A Ben-Dor, N Sampas, E Dougherty, E Wang, F Marincola, C Gooden, J Lueders, A Glatfelter, P Pollock, J Carpten, E Gillanders, D Leja, K Dietrich, C Beaudry, M Berens, D Alberts, V Sondak, N Hayward, J Trent. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature, 406:536-541, 2001.

MJ Callow, S Dudoit, EL Gong, TP Speed, EM Rubin. Microarray expression profiling identifies genes with altered expression in HDL deficient mice. Genome Research, Vol. 10, No. 12, p. 2022-2029, 2000.

TR Golub, DK Slonim, P Tamayo, C Huard, M Gaasenbeek, JP Mesirov, H Coller, ML Loh, JR Downing, MA Caligiuri, CD Bloomfield, ES Lander. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286:531-537, 1999.

CM Perou, SS Jeffrey, M van de Rijn, CA Rees, MB Eisen, DT Ross, A Pergamenschikov, CF Williams, SX Zhu, JCF Lee, D Lashkari, D Shalon, PO Brown, D Botstein. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci, 96:9212-9217, 1999.

Publicly Available Data Sets

Stanford Microarray Database http://genome-www5.stanford.edu/MicroArray/SMD/

Datasets for exploring classification of tumors by gene expression profiles (includes the Alizadeh et al. and Bittner et al. datasets) are available at http://lpgprot101.nci.nih.gov:8080/GEAW

Methods (Not Comprehensive)

Technical Reports 576, 578, 584, and 589 from the UC Berkeley Statistics Department: http://www.stat.berkeley.edu/tech-reports/index.html

BS Everitt. Cluster Analysis, 3^rd edition. London: Arnold, 1993.

CA Blasbey, GW Horgan. Image Analysis for the Biological Sciences. New York: Wiley, 1995.

DJ Hand. Discrimination and Classification. New York: Wiley, 1981.

T Hastie, R Tibshirani, J Friedman. The Elements of Statistical Learning. New York: Springer, 2001.

AK Jain, RC Dubes. Algorithms for Clustering Data. Englewood Cliffs, New Jersey: Prentice-Hall, 1988.

L Kaufman, P Rousseuw. Finding Groups in Data: an introduction to cluster analysis. New York: Wiley, 1990.

KV Mardia, JT Kent, JM Bibby. Multivariate Analysis. London: Academic, 1979. (or other multivariate analysis book)

B Ripley. Pattern Recognition and Neural Networks. New York: Cambridge University Press, 1996.

WN Venables, BD Ripley. Modern Applied Statistics with S-PLUS, 3^rd edition. New York: Springer, 1999.

PH Westfall, SS Young. Resampling-based Multiple Testing. New York: Wiley, 1993.

Partial List of Useful Web Sites

European Bioinformatics Institute http://www.ebi.ac.uk, and in particular http://industry.ebi.ac.uk/~alan/MicroArray/ (and links therein)

Nature http://www.nature.com/genomics/

Stanford Genomic Resources http://genome-www.stanford.edu

Terry Speed’s Microarray Analysis Group: http://www.stat.berkeley.edu/users/terry/zarray/Html/index.html

Sandrine Dudoit http://oz.berkeley.edu/~sandrine