PUMAdb : About the Database

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Background and Citations

PUMAdb is a project within the Lewis-Sigler Institute for Integrative Genomics of Princeton University. PUMAdb is based on the Stanford Microarray Database (SMD) software package.

If you want to refer to PUMAdb within a publication, please use:

http://puma.princeton.edu

The PUMAdb project is a collaboration with SMD, as mentioned above. Most of the tools and software can referenced in the following SMD publications:

Ball CA, Awad IA, Demeter J, Gollub J, Hebert JM, Hernandez-Boussard T, Jin H, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res 2005 Jan 1;33(1):D580-2
Full text  |  PubMed

Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, Hebert JM, Hernandez-Boussard T, Jin H, Kaloper M, Matese JC, Schroeder M, Brown PO, Botstein D, Sherlock G. The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res 2003 Jan 1;31(1):94-6.
Full text  |  PubMed

Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM. The Stanford Microarray Database. Nucleic Acids Res 2001 Jan 1;29(1):152-5.
Full text  |  PubMed


Database statistics

Various database statistics are available here

External references in the database

The external sources of biological annotation used in the database are listed here.

The PUMAdb system

For comparison (and other suggestions), see SMD's system

Related Database Projects

Many other university microarray projects were initialized with the Stanford package, and so could be considered part of the larger collaboration: