The PhenoGen Informatics web site is not only a microarray repository but also a comprehensive toolbox for analyzing microarray data and researching candidate genes and QTLs.

The site is organized into five major sections which are explained in detail in the corresponding Overview Section:

• Detailed Transcription Information-View exon/probest level data for a gene or gene level data for a genomic region.
• Downloads-Download any public data
• Microarray Analysis Tools (login required)-Tools to normalize, filter, differential expression, cluster, correlate array data.
• Gene Analysis Tools (login required)-Tools to help gain insight into gene annotaion, expression, promoters, exon correlation, homology.
• QTL Tools (login required)-Tools to calculate QTLs, create QTL lists, view QTLs associated with genes.

Click the Overview option above to see examples of what you can do on our site. The options to the right of the Overview are the main areas of the site. The functions with a green background indicate publicly accessible parts of the site, while the remaining functions with the blue background require a login.

Review the current datasets that we have available for public use.

Why do we require a login?

For many of the tools that require a login, there are multiple intermediate steps in the analisys or steps that may take a long time to complete. Logging in, allows you to start a step and come back to the analysis/results at a later time. A login also allows you to upload data to the site and keep it private or to share it with individuals you approve.

Acknowledgements

Funding

We would like to thank the National Institue on Alcohol Abuse and Alcoholism (NIAAA) for continued funding to develop and support this site. The Banbury Fund for supporting the development of this site.

Recombinant Inbred Panels

We are grateful to the following investigators for providing the recombinant inbred panels found on the site.
HXB/BXH Rat RI Panel was provided by Morton Prinz(UC San Diego).
ILSXISS Mouse RI Panel was provided by Thomas Johnson(CU Boulder) and John DeFries(CU Boulder).