The Whole EST Catalog

In the past few years a host of new instruments and tools (and even a few companies) have appeared for creating, imaging, and analyzing arrays. Below is a list of some of the companies that are active in this field, with the caveat that some new products and approaches may have inadvertently been missed. The Expression Data Mining Tool (EDMT) is an intuitive query that sifts through large numbers of gene expression results and identifies those that meet selected criteria based on projects, experiments, and tissue type as well as thresholds for absolute expression levels and expression level changes. Results of queries are displayed in a variety of graphs such as scatter plots, bar graphs, or histograms. The GeneChip Laboratory Information Management System (LIMS) manages and tracks process data, raw data, and probe array results from multiple GeneChip systems or other GATC™ compatible sources. Specific process information such as bar-coded sample identification, operator name, reagent lot numbers, and analysis parameters are captured for each sample as it is routed through the steps of a protocol. BioDiscovery offers ImaGene™ software for capturing gene expression microarray and high-density membrane data and automating the process of measuring and visualizing gene expression data. Using image processing and pattern recognition algorithms, ImaGene locates microarray spots even in irregularly placed arrays and quantifies the values using any number of user-selected methods. Time series experiment in yeast performed by R. J. Cho (R.J. Cho et al, "A genome-wide transcriptional analysis of the mitotic cell cycle", Molecular Cell, 2:65-73, 1998) showing genes with expression patterns similar to CLN1. The Venn diagram sets the color for each gene. Screenshot of GeneSpring software from Silicon Genetics. GeneSpring from Silicon Genetics provides data mining features that work with any organism and any type of quantitative data, such as microarrays, Affymetrix chips, and SAGE. Data can come from a variety of relational databases, flat files, and spreadsheets with a comprehensive choice of normalization options. GeneSpring can intuitively visualize multiple experiments simultaneously, according to physical position, functional classification, as line graphs or histograms, as trees of gene clusters, as ordered lists, scatterplots, or overlaid onto arbitrary pictures. Analysis algorithms include expression level restrictions, as well as more powerful expression pattern comparisons, clustering into dendrograms, and sequence motif comparisons GeneView™ software allows rapid analysis of microarrays. A comprehensive set of tools is included to quantify experimental results. These tools can be applied automatically to facilitate the needs of high-volume users. Conversely, for research applications, users can call upon a variety of analysis tools to extract quantitative or qualitative information to suit their specific needs. Microarray analysis using ArrayVision. Image provided by Imaging Research Imaging Research has developed ArrayVision™ based upon the well-established MCID and AIS imaging platforms. ArrayVision is a user-friendly automated analysis software for genome arrays. It incorporates flexible normalization and background correction, statistical segmentation, metrics and precision quantification. A notable feature of ArrayVision is the Flexible Interpolative Targeting tool, which performs automated alignment of array templates to guarantee the quality of data acquisition and analysis. ArrayVision is fully optimized for fluorescent microarrays. This month, Imaging Research will launch its Statistical Informatics program, which will allow exclusive access to an enhanced version of ArrayVision with a built-in informatics module. This will provide advanced statistical procedures optimized for analyses of expression data; it allows one to specify in advance of an experiment the number of replicates required to detect differential expression of a particular magnitude (for example, 1.5-fold, 2-fold) with specified confidence (for example, 95%, 99%). ArrayVision is also distributed by Molecular Dynamics, Genome Systems (as Genome Discovery) and CLONTECH (as AtlasVision). GEMTools™ software provides tools for managing and analyzing the results of GEM microarray experiments. It utilizes an image recognition algorithm that interprets scanned images and compares them against a library database to identify which genes were differentially expressed in two cell samples and at what intensity. Search and reporting tools provide analysis capabilities such as comparing gene expression across a time series to see the effects of a drug over time. Affymetrix (available from Amersham Pharmacia Biotech) The Affymetrix GeneChip™ probe arrays includes sets of expression arrays for human, murine, and yeast genomes, each sporting over 6000 sequences and which together cover the entire cadre of expressed genes from each genome. The GeneChip Fluidics Station automates the hybridization of nucleic acid target to the probe array cartridge, controlling delivery of reagents and the timing and temperature for hybridization. Each fluidics station can independently process four probe arrays at one time. Affymetrix has partnered with Hewlett-Packard in the production of an array scanner for use with GeneChip probe arrays. The GeneArray™ Scanner uses an argon-ion laser to excite fluorescent molecules incorporated into the nucleic acid target to generate a quantitative hybridization signal. This scanner focuses the laser on 3-micron spots within each of the thousands of probe cells contained on the GeneChip probe array. A high-resolution image of the probe array is displayed in real time during scanning, and fluorescence intensity data is automatically stored in a raw file. Image captured without confocla pinhole (left) and with confocal pinhole (right). Image courtesy of General Scanning, Inc. General Scanning introduced in 1997 the ScanArray™ 3000, an open-architecture confocal laser scanner for microarrays. The ScanArray 3000 Microarray Analysis System uses high numerical aperture confocal optics to achieve high light collection efficiency and to reject substrate artifacts. ScanArray systems will allow for up to four-color experiments on a single microarray and could support potentially over 50 fluorescent dyes. To support high-throughput microarray analysis, the system supports microarray data tracking, batch loading, high-speed data communications, and analysis of microarrays at speeds greater than four times faster than first generation systems. A modular "build to order" architecture allows upgrades to accommodate the rapidly changing requirements of the technology. In approaching this field, General Scanning acknowledges that the full benefits of microarray technology will be realized when detection, analysis and data management processes are optimized to work together. With that goal in mind, General Scanning has been collaborating with companies to insure compatibility of formats, fluorescent labels and data tracking. Genetic MicroSystems (GMS) is positioning itself as "enablers" to the arraying technology by trying to provide high performance instrumentation at affordable pricing. GMS has developed a method of laser scanning digital imaging, called "wide field microscopy", for rapid, high-resolution imaging of fields ranging in size from a portion of a coverslip to an entire microplate. The GMS technology is based on use of a "flying objective lens" utilizing a proprietary low-mass objective lens mounted at the end of an oscillating arm. Other design elements of the GMS confocal scanning microscope include high light collection efficiency and novel electronic circuits for increased sensitivity and dynamic range, 10 microns per pixel resolution, ability to scan glass slides or substrates, multi-color excitation and emission channels, large 22 x 60 mm single pass scanning field of view, 16-bit dynamic range. Genetic Microsystems also provides an arrayer to array biological samples using a novel "pin and ring" technology on a variety of substrates. This machine allows deposition of any fluid or suspension in spots ranging in diameter from 50 to 300 microns. Genometrix has a multiplexed microarray manufacturing system capable of producing low to medium density (10s to low 1000s) oligo or cDNA probe arrays. Microarrays can be printed within the wells of conventional 96 well microplates or on microscope slides that contain 10 to 18 arrays per slide. The microarrays are priced as low as $10 per array, depending on volume and complexity. Genometrix has developed a patented lensless CCD imaging technology that is capable of high throughput (1-30 seconds), ultrasensitive detection (subattomole), and quantitative imaging (16 bits) of molecules labeled with chemiluminescent or fluorescent reporter groups. The Bioscanner™ is much like a copying machine whereby the microarray is placed directly on the sensor surface. Genomic Solutions offers the GeneTAC™ Biochip Analyzer, a CCD camera with high-intensity, narrow-band illumination for detecting spots of various diameters from low- to medium-density arrays labeled with CY3 or CY5. The system also contains the company s Visage™ High Density Grid Analyzer, which can calculate the hybridization levels of over 200,000 spots in high-density array images. Genosys has recently introduced an expression array for E.coli, the Panorama E.coli Gene Arrays, which contain over 4,000 spots, representing the entire cohort of expressed genes from the E.coli genome (strain K-12 {MG1655}). Combined with standard imaging systems (phorphor screen or fluoro imagers) and software for array analysis, these arrays can provide a way of comparing the expression levels of all 4,290 genes in a single hybridization experiment. Each spot on the E.coli gene arrays contains ten nanograms of an entire, amplified open reading frame, arrayed at a 2 mm spacing. Genosys also provides cDNA-labeling primers for probe preparation, which give, according to the company, higher signal sensitivity compared to random primers. Soon to be released are arrays for human cytokines and B. subtilis. Genzyme Molecular Oncology provides complete analyses of gene expression using SAGE technology (see box on right). Its service offering include acquisition of tissue, preparation and sequencing of SAGE transcripts, and data analysis. All data generated in a custom analysis can be proprietary to meet individual needs. (www.genzyme.com/prodserv/molecular_oncology/sage/prodserv.htm) The GEMTools element display shows the differential expression of each element on the GEM array, including a visual representation of expression intensity. Image courtesy of Incyte/Genome Systems. Incyte provides proprietary microarrays (LifeGEM™, ZooGEM™ and PathoGEM™) as well as public domain microarrays, PD GEM. Gem microarrays are constructed by the chemical bonding of cDNA s to glass. GEM technology can fit 10,000 unique genes on a single array, each gene 500-5000 bases long. Incyte's LifeArray™ software manages and analyzes data resulting from microarray hybridization experiments. It includes a searchable database which can be loaded with microarray experimental results from a variety of formats. TeleChem International is developing tools and technologies for the microarray industry, including a proprietary, high-precision microarray fabrication ("ChipMaker") technology. ChipMaker uses state-of-the-art surface contact printing to construct high density arrays. TeleChem also offers proprietary microspotting and hybridization buffers, including Unihyb, which expedites mismatch detection with microarrays. Supporting tools including wash stations and hybridization cassettes. Author Bob Klevecz may be reached at and Laura DeFrancesco at ldefrancesco@the-scientist.com. ALTERNATIVE TO CHIP ARRAYS While garnering much of the attention, the chip array is not the only technology for unraveling the complexities of gene expression. Several years ago, researchers at Johns Hopkins University developed a method called serial analysis of gene expression (SAGE) that allows the quantitative analysis of thousands of transcripts simultaneously1. The SAGE method is based on the isolation of unique sequence tags from individual transcripts and concatenation of tags serially into long DNA molecules. Rapid sequencing of concatemer clones reveals individual tags and allows quantitation and identification of cellular transcripts. As a first demonstration of the approach, SAGE was used to analyze gene expression in the human pancreas, revealing an expression profile characteristic of pancreatic function and identifying new pancreatic transcripts1. Subsequently SAGE has been used to characterize the set of genes expressed from the yeast genome2. Analysis of 60,633 transcripts from S. cerevisiae has identified 4665 unique transcripts, comprising 1981 known genes and 2684 uncharacterized genes. Gene expression levels ranged over three orders of magnitude, from 0.3 to over 200 transcript copies per cell. Integration of positional information with gene expression data allowed the generation of chromosomal expression maps and the precise identification of expressed genes. Surprisingly, several hundred new genes were identified that had not been previously predicted by analysis of the complete yeast genome sequence. More recently SAGE has been applied to the analysis of gene expression profiles in gastrointestinal cancers3, to the identification of transcriptional targets of p53 that regulate apoptosis4, and mediate G2 arrest5, and to connecting the APC tumor suppressor and MYC oncogenic pathways6. The expectation is that the identification of such differentially expressed genes will furnish insights into the pathophysiology of cancer and open up possibilities for useful diagnostic and therapeutic approaches. While the commercial application of SAGE is being handled through Genzyme Molecular Oncology, academic researchers interested in using this technology can obtain detailed protocols from the SAGE group at The Johns Hopkins Oncology Center (www.sagenet.org). V.E.Velculescu, et al., "Serial Analysis Of Gene Expression", Science 270, 484-7, 1995. V.E. Velculescu et al., "Characterization of the yeast transcriptome", Cell, 88:243-51, 1997. L. Zhang et al., "Gene expression profiles in normal and cancer cells", Science, 276:1268-72, 1997. K. Polyak, et al., "A model for p53 induced apoptosis", Nature 389, 300-5, 1997. H. Hermeking et al., "14-3-3 Is a p53-Regulated Inhibitor of G2/M Progression", Molecular Cell 1:3-11, 1997. T.-C. He et al., Identification of c- MYC as a Target of the APC Pathway", Science, 281:1509-12, 1998. Chromosomal expression map for S. cerevisiae. Individual yeast genes were positioned on each chromosome according to their open reading frame start coordinates. Abundance levels of tags corresponding to each gene are displayed on the vertical axis (+ strand above axis, - strand below). Reprinted with permission from: V.E. Velculescu, et al., "Characterization of the yeast transcriptome", Cell 88, 243-251, 1997. L. Zhang et al., "Gene expression profiles in normal and cancer cells", Science, 276:1268-72, 1997. A.Y. Liu et al., "Cell-cell interaction in prostate gene regulation and cytodifferentiation", Proceedings of the National Academy of Sciences, 94:10705-10, 1997 R.J. Cho et al., "A genome-wide transcriptional analysis of the mitotic cell cycle", Molecular Cell, 2:65-73, 1998. R.R. Klevecz et al., "Cellular clocks and oscillators", International Review of Cytology, 86:97-128 1984. J. Creanor and J.M. Mitchison, "Nucleoside diphosphokinase, an enzyme with step changes in activity during the cell cycle of the fission yeast Schizosaccharomyces pombe. I. Persistence of steps after a block to the DNA-division cycle" Journal of Cell Science, 86:207-15, 1986. R.R Klevecz , "Phenotypic heterogeneity and genotypic instability in coupled cellular arrays" Physica D: in press Dec 1998 Hieter P, Boguski M. "Functional genomics: it's all how you read it", Science 278:601-2, 1997. Table of Products for Making and Analyzing High Density Arrays

The Whole EST Catalog

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