Genomatix Microarray Analysis Pipeline achieves Affymetrix GeneChip compatible™ status

November 29, 2005

Genomatix Software GmbH today announced that it has achieved GeneChip-compatibleTM status for several products with the Affymetrix Inc. (Nasdaq: AFFX) GeneChip® microarray platform and that it has joined Affymetrix GeneChip-compatible Applications Program, which provides customers with a broad spectrum of software solutions for biomedical research and development. As a GeneChip-compatible software provider, Genomatix is committed to seamlessly integrating its entire microarray analysis pipeline with the Affymetrix technology.

The Genomatix line of products which achieved GeneChip-compatibleTM status consists of ChipInspector, ChipInspector TL, ElDorado, GEMS Launcher, and BiblioSphere PathwayEdition. With those products Genomatix provides a broad set of solutions for Affymetrix GeneChip users, including analysis of data from Affymetrix whole-genome tiling and exon arrays.

"We are proud of having met the high standards of Affymetrix and earning GeneChip-compatibleTM status. The tight integration of our microarray analysis pipeline with the Affymetrix platform will stimulate exciting new results in both basic and applied biomedical R&D," said Klaus May, Director of Sales and Marketing at Genomatix. "Especially in conjunction with the new Affymetrix tiling and exon array technology, I expect that our tools will drive far greater understanding of genomic organization and transcriptome regulation."

"Affymetrix is pleased to be working with Genomatix in their efforts to develop advanced tools for analyzing GeneChip data," said Steve Lincoln, vice president of Informatics at Affymetrix. "We are particularly excited to see the emergence of next-generation commercial software which can help bring unprecedented levels of genomic resolution into the hands of applied biomedical researchers."
About Genomatix Software
ChipInspector applies a new approach to identify significantly regulated genes, which can resolve alternative transcription from the same gene locus. ChipInspector is based on analysis of single probes rather than the standard probe set approach, which pools groups of probes into a probe set. The single-probe approach became possible due to the up to date high quality genome annotation contained in Genomatix´ ElDorado system.

ChipInspectorTL shares the single probe approach with ChipInspector but is tuned for analysis of the new Affymetrix genomic tiling technology. Tiling probes with significantly changed expression values are annotated based on ElDorado and mapped to the genomic regions. Several clustering features facilitate identification of tiling probes with similar profiles.

ElDorado is a genome annotation and analysis system with up to date annotations for currently 12 different organisms. It is completely based on proprietary mapping, contains patent pending comparative genomics and the worlds largest database of quality checked promoter DNA sequences.

GEMS Launcher, a software and database package for analysis of gene regulatory mechanisms on the molecular level, includes over 20 different software tools for promoter analysis, high quality data on transcription factor binding sites (TFBS), promoter modules and a gateway to the world's largest database of quality assessed mammalian promoters. The tools are suitable to detect common organization in sets of promoters e.g. as derived from transcripts/genes identified by ChipInspector. Subsequently promoter database searches can detect additional potentially co-regulated genes. The tools using TFBS predictions are based on the gold standard MatInspector, which is included in the package. GEMS launcher is currently used by more than 26.000 researchers worldwide.

BiblioSphere PathwayEdition is based on independent data sources such as the Genomatix Knowledge Base, and sequence analysis. The system allows dynamic data-driven gene network construction and automatically creates the entire network of biological connections between input and correlated genes. BiblioSphere PE supports the user with various tools to facilitate focusing on functional sub-nets in order to identify the most relevant biological context. There is no size limit for networks to be analyzed and integration of sequence analysis provides additional independent lines of evidence. This feature is based on Genomatix' proprietary genome annotation and its unique promoter and transcription factor binding site database.

About the Affymetrix Developers Network (ADN)
Through one of the largest third-party software developer communities within the life science industry, Affymetrix works with its partners to provide a broad spectrum of solutions for leveraging gene expression and genetic variation analysis in both biomedical research and development. Membership in ADN is free of charge for both commercial and academic software developers. For more information please visit Visit the GeneChip-compatible Software Solutions Catalog at

About Genomatix Software GmbH:
Genomatix started 1997 as a spin-off from the GSF - National German Research Center for Environment and Health. The company developed a multilayer integrative approach aimed at understanding differential gene expression and regulation at the molecular level. Genomatix offers a complete solution from microarray analysis: Starting with the raw expression data (e.g. CEL files) complete biological networks are reconstructed from the data employing literature and pathway knowledge bases , combined with sequence-level analysis of transcriptional co-regulation. Genomatix thus improves understanding of biological mechanisms under different conditions and stimuli and helps to discover new context from biological data. Genomatix published more than 160 peer reviewed scientific papers, which are cited in more than 3,700 papers. More than 24,000 researchers worldwide currently apply Genomatix tools and databases. For more information about Genomatix, please visit the company's website at About Affymetrix:

Affymetrix scientists invented the world's first high-density microarray in 1989 and began selling the first commercial microarray in 1994. Since then, Affymetrix GeneChip® technology has become the industry standard in molecular biology research. Affymetrix technology is used by the world's top pharmaceutical, diagnostic and biotechnology companies as well as leading academic, government and not-for-profit research institutes. More than 1,300 systems have been installed around the world and nearly 3,000 peer-reviewed papers have been published using the technology. Affymetrix' patented photolithographic manufacturing process provides the most information capacity available today on an array, enabling researchers to use a whole-genome approach to analyzing the relationship between genetics and health. Affymetrix is headquartered in Santa Clara, Calif., with manufacturing facilities in Sacramento, Calif., and Bedford, Mass. The company maintains important sales and marketing operations in Europe and Asia and has about 1,000 employees worldwide. For more information about Affymetrix, please visit the company's website at

Genomatix Software GmbH

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