PUMAdb : Princeton University MicroArray database

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The Princeton University MicroArray database (PUMAdb) stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, PUMAdb provides interfaces for data retrieval, analysis and visualization.

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Princeton researchers and their collaborators should register for a database account. Data is released to the public at the researcher's discretion or upon publication. If you are a world user, and are just trying to reach viewable data, either view our publications page or activate a world session.

PUMA Access: Access to non-public data is limited to registered Princeton researchers and their collaborators. Please see PUMAdb Registration for more specific information. If you have further questions regarding access, please e-mail the Princeton Microarray Database curators.

Announcements

2008-04-04 : Notice - Some Agilent print names have been modified within the database to improve standardization. This may effect data loading from older batch files. Please consult the print list for the list of updated print names for your chosen platform.

2007-11-05 : Notice - Due to popular demand, the default column retrieved for GenePix result sets has been changed to be median-based instead of mean-based. The new default is Log (base 2) of the ratio of the medians of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)]. If this is an inconvenience, or you have any questions, please send a message to array@genomics.princeton.edu .

2007-11-05 : New Features added!

  1. User defaults : the ability to save your selections on frequently used forms.
  2. Preliminary support for yeast tiling array data, including both CEL and SNPScanner result sets
  3. and more...

2007-10-31 : Notice - Experiment sets that are annotated as a "temporary workset" and are over a month old are now being cleaned up.


Recent Publications

2008-04-15 : Gene-Environment Interaction in Yeast Gene Expression Smith EN, Kruglyak L (2008) PLoS Biol 6(4): e83 doi:10.1371/journal.pbio.0060083

2007-12-31 : Microarray Data Mining: A Novel Optimization-Based Iterative Clustering Approach to Uncover Biologically Coherent Structures. Tan et al. 2007 (submitted)



Project Funding and Support: PUMAdb is funded in part by the National Institute of General Medical Sciences (NIGMS) [NIH grant P50 GM071508]. PUMAdb is a project within the Lewis-Sigler Institute for Integrative Genomics at Princeton University. Software and schema are based on the Stanford Microarray Database software package, and ongoing development remains a collaboration with this group.

Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.