• Investigator Login
• Deadlines and Application Procedures
• NIAID PFGRC Site
• NIDCR (Dental Pathogens)
• Available Microarrays
• Description of Annotation Files
• Description of the EASE Archive
• Description of Controls
• Instructions for Downloading Annotations
• Forms and Documentation
• Laboratory Protocols
• Frequently Asked Questions

The NIAID sponsored Pathogen Functional Genomics Resource Center (PFGRC) at the J. Craig Venter Institute is pleased to announce the release of three new, free open-source software tools: Magnolia, Ginkgo and APEX. Magnolia is a microarray data management and export system for researchers who use PFGRC microarrays. The software greatly simplifies the tasks of organizing experimental data and submitting it to a public data repository. Ginkgo is a Comparative Genomic Hybridization (CGH) and expression microarray data analysis package. Several normalization, data filtering and imputation, and replicate microarray functions are implemented in an intuitive graphical framework. The APEX tool is an implementation of the Absolute Protein Expression quantitation technique. It can compute protein abundance values for LC-MS/MS proteomics datasets, quantifying hundreds or thousands of proteins. Links to additional information on each of these new software tools is available from the PFGRC's bioinformatics page.

The National Institute of Allergy and Infectious Diseases (NIAID) supported Pathogen Functional Genomics Resource Center (PFGRC) designs, constructs, and distributes glass slide DNA microarrays for pathogens and biodefense related organisms (Select A-C agents). Currently, the PFGRC supports DNA microarrays for the 38 organisms listed here. In continuing its efforts to provide the infectious disease and biodefense communities with the microarray resources most relevant to their research efforts, the PFGRC is soliciting input for selection of its next set of reference/species microarrays. The criteria for organism selection may be found here.

Mycobacterium smegmatis version 3

Slide Description

Annotation Files

The PFGRC provides annotation information in the following formats:

• Tab-delimited: Which can be opened with most commercial spreadsheet programs.
• GenePix Array List (GAL) format: For use with the "GenePix Pro" application. More information about the GAL file format can be found here.
• Ann format: For use with JCVI Spotfinder and JCVI MEV.
• More information about the format of the annotation files can be found here.
• The EASE TM4 archive is a zip file archive used in the TM4 suite of applications. More information about this file can be found here.

Spotfinder Parameters

The following parameters are for use with JCVI's supported microarray analysis TM4 suite. More information regarding Spotfinder can be found here.