Thursday, August 03, 2000

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Oncology.Com Gene Chips Yield Genetic Profile of Metastatic Melanoma
"In the first study, researchers headed by Edwin A. Clark, Ph.D., and Richard O. Hynes, Ph.D., of the Massachusetts Institute of Technology used human and mouse oligonucleotide microarrays to identify several genes involved in the progression of human melanoma cells to a metastatic phenotype.

One of these genes, which codes for a GTPase called RhoC, enhanced the metastatic capacity of melanoma cells by 50 times when overexpressed.

In the other study, 28 researchers around the world led by Jeffrey Trent, Ph.D., of the National Human Genome Research Institute, applied gene expression profiling to almost 7,000 genes in cutaneous malignant melanoma tumors from 40 patients. Mathematical analysis of the profiling data revealed a cluster of 19 tumors that differed from the other 21 in the expression of about 500 genes.

Subsequent analysis of the medical histories of the patients in the cluster revealed that their tumors were significantly less aggressive than those of the patients outside the cluster. "

redux [05.24.00]
Nature One-stop shop for microarray data
"With the advent of DNA microarray and 'chip' technologies...gene expression in an organism can be examined on a genomic scale, allowing the transcription levels of many genes to be measured simultaneously2. For instance, we can study the effects of a compound (such as a drug) on the level of expression of many genes...With gene expression, context is everything: without it, the information is meaningless. For example, the precise stage of a tumour sample could have a crucial bearing on the interpretation of expression measurements. This context can be infinitely detailed, and it is this detail that must be captured in gene-expression studies.

The bioinformatics underlying the management of these huge volumes of data are crucial if any sense is to be made of gene-expression experiments. A single microarray experiment looking at 40,000 genes from 10 different samples, under 20 different conditions, produces at least 8,000,000 pieces of information."

"It is time to create a public repository for microarray data, with standardized annotation (see Box 2, overleaf). But this is a complex and ambitious project, and is one of the biggest challenges that bioinformatics has yet faced. Major difficulties stem from the detail required to describe the conditions of an experiment, and the relative and imprecise nature of measurements of expression levels. The potentially huge volume of data only adds to these difficulties. However, it is this very complexity that makes an organized repository necessary.

Important tasks to be undertaken include: (1) agreement on the essential information that should be reported for a microarray experiment; (2) definition of ontologies and an extensible, structured document format to capture these data and their semantics; (3) production of a database to store these documents; and (4) development of tools for searching documents in a database and using the semantic context to allow comparisons and sophisticated queries."

redux [07.01.00]
Stanford Medical Informatics Preprint Archive CLEAVER : analyzing microarray data using known biological categories
"Initial efforts in microarray data analysis have focused on clustering methods, but there is increasing interest in the use of traditional classification techniques. We have developed a publicly available web-site to provide investigators easy access to both types of computational tools. Our site can be found at the URL http://classify.stanford.edu/. "

Cleaver Classification of Expression Arrays Version 1.0
"The Cleaver (Classification of Expression Array Version 1.0) internet site provides a variety of tools to assist in the analysis of microarray expression data. It provides facilities for visualization, classification, and clustering. All computations are done on the server side; most of the strategies take no longer than five to ten minutes to compute. All strategies ask users to upload a number of data files and conducts calculations on them."

"The site curators will not under any circumstances exam data that is being uploaded unless requested by the user to do so. All data is deleted after 24 hours. The data is viewable by anyone with the right unique directory code – if this is kept private, the data is secure – as our server does not permit surfing of these directories. The Cleaver site otherwise maintains all of the security that the PharmGKB server employs."

Gene-Chips.Com Monitoring the Genome on a Chip
"Welcome to the Genome Chip (DNA Microarray) Web site! This simple, printer-friendly site has been created and maintained by Leming Shi, Ph.D. You'll find the basics on DNA microarray technology and a list of academic and industrial links related to this exciting new technology. Your comments, corrections, and suggestions are welcome. Please help me make this site more useful to you and many other visitors."