Compendia Bioscience

Compendia Bioscience was founded by Arul Chinnaiyan and Dan Rhodes in February 2006 with the goal of building a commercial version of Oncomine™ that would have a greater ability to impact drug development and clinical practice. Compendia licensed Oncomine and related technologies from the University of Michigan in February of 2006, and signed contracts with its first customers in March of 2006. In its first year, Compendia:

Completed funding agreements providing seed capital for company formation, initial sales marketing and customer acquisition, and development of customer support processes.
Completed formation of an experienced entrepreneurial management team with decades of experience in leading life science and software industry companies such as Spotfire, Gene Logic, Celera, and i3 Statprobe, Genetics Squared.
Acquired its first 10 customers, including 8 of the top 20 oncology drug companies.

In 2007, Compendia Bioscience has assumed full responsibility for providing support and product enhancements for the academic and non-profit versions of Oncomine and Oncomine Concepts Map. Additionally, in March, Compendia launched Oncomine Enterprise Edition 1.0 for deployment to multiple commercial customers. This year Compendia's successes include a growing list of marquee customers, significant improvements to our product and content, one of the largest SBIR grants of the year from the National Cancer Institute, a Product Innovator of the Year Award from the Michigan Business Review, and the development of a talented and motivated core team.



	Oncomine was developed between 2003 and 2006 by academic researchers at the University of Michigan: October 2003 Oncomine 1.0 consisted of 40 microarray data sets and nearly 100 pre-computed differential expression analyses. This version also included analysis tools designed to allow users to query differential expression of a gene across all the collected data sets. October 2004 Oncomine 2.0 increased the number of analyzed data sets to 65 and added a co-expression module. In addition, an improved user interface was developed, and scalable vector graphics (SVG) was adopted for visualizing gene expression data and analyses. Enrichment analysis was added to a later version of Oncomine 2.0. January 2006 Oncomine 3.0 included significant additions in data and functionality. A semi-automated data pipeline was developed that allowed for a substantial increase in the number of collected data sets to 118, and the number of profiled cancer and normal tissue samples to nearly 10,000. In addition, more than 1000 gene expression signatures were derived by grouping the samples based on curated sample facts ranging from cancer diagnosis, transforming mechanism, and patient survival. Additional analysis methods, including Molecular Concepts analysis, Meta-analysis, and Cancer Outlier Profile Analysis (COPA) were also developed. February 2006 Oncomine and related technologies licensed to newly-formed company, Compendia Bioscience. May 2006 Number of collected datasets increased to 144 with more than 12,000 tissue profiles. August 2006 Oncomine 3.1 is released including several feature updates and another large increase in the number of datasets (209) and tissues profiled (14,000+) including first cell-line datasets. October 2006 Beta release of Oncomine Enterprise Edition providing a secure web service for customers to integrate proprietary data and public domain data for analysis and insight. December 2006 Number of collected datasets increased to 264 with more than 18,000 tissue profiles. March 2007 Release of Oncomine Enterprise Edition 1.0 for deployment at multiple commercial customers allowing for integration of private expression data with the public data already available in Oncomine. April 2007 Oncomine 3.2.1 providing integration with Ingenuity’s IPA application for Oncomine Professional customers. Will be included in future editions of Oncomine Research Premium Edition. May 2007 Oncomine 3.2.2 and OCM 0.9 – Academic Preview of Oncomine Concepts Map. A signature-centric application that leverages more than 1,000 cancer signatures generated from Oncomine and a database of more than 20,000 molecular concepts gathered from diverse sources worldwide. Oncomine 3.2.2 is the first release fully supported by Compendia Bioscience for the academic community. June 2007 Oncomine v3.3 released with MyFilters, a powerful new customization tool, allowing users to upload gene lists that can be utilized as custom filters throughout Oncomine. Oncomine Concepts Map Edition v1.0 released with gene sets as a common language to compare and link disparate biological concepts. Gene signatures grow to nearly 7,000. August 2007 23 highly curated data sets — representing over a thousand microarray experiments — are added to the Oncomine database with nearly half of the new studies containing sample data not available by direct download from public repositories. September 2007 Oncomine v3.5 improves user experience by adding a context sensitive help system, quickstart guides, updated online demos, and automated password retrieval. OCM v1.1 introduces the Oncomine Cluster, a set of genes that are strongly correlated with each other (>0.5) within a single study in the Oncomine database. October 2007 Oncomine™ Research Premium Edition includes custom gene filters, integration with Ingenuity Pathway Analysis software and full support for Oncomine Concepts Map, including the ability to upload custom and proprietary concepts in a secure environment. December 2007 Oncomine v3.6 incorporates aCGH data in addition to a complete remapping of reporters to genes improving accuracy. Highly curated data from 35 additional studies are made available; more than 34% of these new studies contain data not available from GEO.