Research Articles

Oligonucleotide Microarrays (GeneChips)

Yeast Expression monitoring by hybridization to high-density oligonucleotide arrays Lockhart et al. (1996) Nat. Biotechnol. 14, p. 1675 Genome-wide expression monitoring in Saccharomyces cerevisiae Wodicka et al. (1997) Nat. Biotechnol. 15, p. 1359 A genome-wide transcriptional analysis of the mitotic cell cycle Cho et al. (1998) Mol. Cell 2, p. 65 Dissecting the regulatory circuitry of a eukaryotic genome Holstege et al. (1998) Cell 95, p. 717 Direct allelic variation scanning of the yeast genome Winzeler et al. (1998) Science 281, p. 1194 Global response of Saccharomyces cerevisiae to an alkylating agent Jelinsky and Samson (1999) Proc. Natl. Acad. Sci. USA 96, p.1486 Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast Wyrick et al. (1999) Nature 402, p. 418 Finding DNA regulatory motifs within unaligned non coding sequences clustered by whole-genome mRNA quantitation Roth et al. (1998) Nat. Biotechnol. 16, p. 939 Redundant roles for the TFIID and SAGA complexes in global transcription Lee et al. (2000) Nature 405, p. 701 Regulatory Networks Revealed by Transcriptional Profiling of Damaged Saccharomyces cerevisiae Cells: Rpn4 Links Base Excision Repair with Proteasomes Jelinski et al. (2000) Mol. Cell. Biol. 20, p. 8157

Mammals Molecular classification of cancer: class discovery and class prediction by gene expression monitoring Golub et al. (1999) Science 286, p. 531 Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays Hacia et al. (1999) Nat. Genet. 22, p. 164 Effectors of a developmental mitogen-activated protein kinase cascade by expression signatures of signalling mutants Madhani et al. (1999) Proc Natl. Acad. Sci. USA 96, p. 12530 Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation Travers et al. (2000) Cell 101, p. 249 Gene-expression profile of the ageing brain in mice Lee et al. (2000) Nat. Genet. 25, p. 294 Widespread aneuploidy revealed by DNA microarray expression profiling Hughes et al. (2000) Nat. Genet. 25, p. 333 Monitoring cellular responses to listeria monocytogenes with oligonucleotide arrays Cohen et al. (2000) J. Biol. Chem. 275, p. 11181 Analysis of p53-regulated gene expression patterns using oligonucleotide arrays Zhao et al. (2000) Genes Dev. 14, p. 981 Genomic analysis of metastasis reveals an essential role for RhoC Clark et al. (2000) Nature 406, p. 532 Regional and strain-specific gene expression mapping in the adult mouse brain Sandberg et al. (2000) Proc Natl. Acad. Sci. USA 97, p. 11038

PCR Microarrays

Yeast & Plants Yeast microarrays for genome wide parallel genetic and gene expression analysis Lashkariet al. (1997) Proc. Acad. Natl. Sci. USA 94, p. 13057 Exploring the metabolic and genetic control of gene expression on a genomic scale DeRisi et al. (1997) Science 278, p. 680 The transcriptional program of sporulation in budding yeast Chu et al. (1998) Science 282, p. 699 Comprehensive identification of cell cycle regulated genes of the yeast Saccharomyces cerevisiae by micro array hybridization Spellman et al. (1998) Mol. Biol. Cell 9, p. 3273 Ploidy regulation of gene expression Galitski et al. (1999) Science 285, p. 251 Systematic changes in gene expression patterns following adaptive evolution in yeast Ferea et al. (1999) Proc. Natl. Acad. Sci. USA 96, p. 9721 Action of BTN1, the yeast orthologue of the gene mutated in Batten disease. Pearce et al. (1999) Nat. Genet. 22, p. 55 Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast Lyons et al. (2000) Proc. Natl. Acad. Sci. USA 97, p. 7957 Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth Zhu et al. (2000) Nature 406, p. 90 The chromo domain protein Chd1p from budding yeast is an ATP-dependent chromatin-modifying factor Tran et al. (2000) EMBO J. 19, p. 2323 Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae  Gerton et al. (2000) Proc. Natl. Acad. Sci. USA 97 p.  11383 Coordinated plant defense responses in Arabidopsis revealed by microarray analysis  Schenk et al. (2000) Proc. Natl. Acad. Sci. USA  97 p. 11655 Identification of the Copper Regulon in Saccharomyces cerevisiae by DNA Microarrays Gross et al. (222) J. Biol. Chem. 275 p. 32310

Nematodes & Mammals The transcriptional program in the response of human fibroblasts to serum Iyer et al. (1999) Science 283, p. 83 cDNA microarrays detect activation of a myogenic transcription program by the Pax3-Fkhr fusion oncogene. Kahn et al. (1999) Proc. Natl. Acad. Sci. USA 96, p. 13264 Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling Alizadeh et al. (2000) Nature 403, p. 503 Systematic variation in gene expression patterns in human cancer cell lines Ross et al. (2000) Nat. Genet. 24, p. 227 A gene expression database for the molecular pharmacology of cancer Scherf et al. (2000) Nat. Genet. 24, p. 236 Analysis by High Density cDNA Arrays of Altered Gene Expression in Human Intestinal Epithelial Cells in Response to Infection with the Invasive Enteric Bacteria Salmonella Eckman et al. (2000) J. Biol. Chem. 275, p. 14084 Gene microarray identification of redox and mitochondrial elements that control resistance or sensitivity to apoptosis Voehringer et al. (2000) Proc. Natl. Acad. Sci. USA 97, p. 2680 Molecular classification of cutaneous malignant melanoma by gene expression profiling Bittner et al. (2000) Nature 406, p. 536 Molecular portraits of human breast tumours Perou et al. (2000) Nature 406, p. 747 A Global Profile of Germline Gene Expression in C. elegans Reinke et al. (2000) Mol Cell 6, p. 605

Bioinformatics

Cluster analysis and display of genome-wide expression patterns Eisen et al. (1998) Proc. Natl. Acad. Sci. USA 95, p. 14863 MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling. Tanabe et al. (1999) Biotechniques 27, p. 1210-4, 1216-7 Knowledge-based analysis of micro array gene expression data by using support vector machines Brown et al. (2000) Proc. Natl. Acad. Sci. USA 97, p. 262 Fundamental patterns underlying gene expression profiles: Simplicity from complexity Holter et al. (2000) Proc. Natl. Acad. Sci. USA 97, p. 8409 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns Hastie et al. GenomeBiology, August 4, 2000. Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis Bussemaker at al. (2000) Proc. Natl. Acad. Sci. USA 97, p. 10096

Genomic deletion projects

Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis Winzeler et al. (1999) Science 285, p. 901 Large-scale analysis of the yeast genome by transposon tagging and gene disruption Ross-Macdonald et al. (1999) Nature 402, p. 413

Reviews

The Chipping Forecast Nature Genetics Supplement 21, (1999) DNA Chips: promising toys have become powerful tools Gerhold et al. (1999) TIBS 24, p. 168 Expression profiling in cancer using cDNA microarrays Kahn et al. (1999) Electrophoresis 20, p. 223 Analysis of gene expression in single cells Freeman et al. (1999) Curr. Opin. Biotechnol.10, p. 579 Observing the living genome Ferea and Brown (1999) Curr. Opin. Genet. Dev. 9, p.715 Mutational analysis using oligonucleotide microarrays Hacia and Collins (1999) J. Med. Genet. 36, p. 730 Fluorescence-based expression monitoring using microarrays Winzeler et al. (1999) Methods Enzymol. 306, p.3 Identifying expressed genes Martin and Pardee (2000) Proc. Natl. Acad. Sci. USA 97, p. 3789 Genomics, gene expression and DNA arrays Lockhart and Winzeler (2000) Nature405, p.827 Biomedical discovery with DNA arrays Richard Young (2000) Cell102, p.9 Host-pathogen studies in the post-genomic era Paul Kellam, GenomeBiology, August 4, 2000 Does massively parallel transcriptome analysis signify the end of cancer histopathology as we know it? Aparicio et al. GenomeBiology, September 15, 2000

Online info

General array links

http://www.gene-chips.com/ http://www.microarrays.org/ http://www.nature.com/genomics/links/index.html

More literature

http://www.affymetrix.com/resources/scientific_paper.html http://www.nature.com/genomics/papers/index.html http://linkage.rockefeller.edu/wli/microarray/

Online expression databases

http://www.ncgr.org/research/genex/ http://www.sigenetics.com/Products/Genex/index.html http://www.ebi.ac.uk/arrayexpress/ http://arep.med.harvard. edu/ExpressDB http://www.ncbi.nlm.nih.gov/geo/ http://www.mips.biochem.mpg.de/cgi-bin/proj/expression/start.pl

Genomes

http://www.ncbi.nlm.nih.gov:80/PMGifs/Genomes/allorg.html http://www.tigr.org/ http://www.genome.ad.jp/kegg

Annotation

http://www.geneontology.org/ http://stein.cshl.org/das/ http://www.ensembl.org/ http://grail.lsd.ornl.gov/tools/channel/

Yeast

http://genome-www.stanford.edu/Saccharomyces http://www.mips.biochem.mpg.de

Human

http://www.ensembl.org/ http://www.nhgri.nih.gov/HGP

Cancer

http://www.ncbi.nlm.gov/CGAP http://www.icr.ac.uk/molcarc/teams/molpath.html

Online Journals

http://www.biomedcentral.com/ http://genomebiology.com/