Microarray Suggestion Criteria
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.
Bioinformatics
The Bioinformatics department works closely with the staff in all PFGRC programs including DNA microarray and gene expression, the Invitrogen Gateway® Clone Resource, Comparative Genomics, and Proteomics. Their directive is to provide software, technical support and analysis expertise to advance the production and scientific objectives of the PFGRC and the pathogen research community. Several software tools have been released to the community under open-source licenses, including the TM4 microarray software suite and the LEM (Linear Expression Maps) and NonpaR (Nonparametric Statistical Tests) modules. The implementation of a microarray annotation pipeline and internal tool "Sanim" streamlined the process of creating current annotation files for every PFGRC microarray design. EASE filesystems for these microarrays supplement the annotation files, providing GO terms, cellular roles and PFAMs, and facilitate the analysis of functional roles. A number of comparative analysis tools have been developed to facilitate Comparative Genomics research including the development of a set of filtering tools designed to identify and distinguish valid and spurious SNP calls when using Affymetrix GeneChips for the purpose of resequencing, and data normalization and classification tools for CGH experiments.
The table below summarizes and links to bioinformatics resources provided by the PFGRC.
Project Description |
Reagents and Resources |
Collaborators |
TM4: Comprehensive Microarray Software Suite for Data Management and Analysis |
John Quackenbush and the Computational Biology and Functional Genomics Lab, Dana Farber Cancer Institute |
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LEM (Linear Expression Maps): Visualizing Gene Expression on a Chromosomal Coordinate Map |
LEM Module, implemented in the MeV Application (TM4 Suite) and Source Code |
|
NonpaR: Four Nonparametric Statistical Tests for Common Microarray Experimental Designs |
NonpaR Module, implemented in the MeV Application (TM4 Suite) and Source Code |
|
Microarray Annotation Pipeline |
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EASE: Resources for Biological Role Analysis of Gene Lists |
EASE Filesystems for PFGRC Microarrays (including CMR cellular roles, GO terms and PFAM annotations) |
|
Genotyping and SNP detection of Streptococcus pneumoniae isolates by resequencing arrays |
Catherine McEllistrem, The University of Pittsburg |
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Whole Genome Resequencing and Single Nucleotide Polymorphism Genotyping of 40 Franciscella tularensis Strains |
F. tularensis comparative analysis tool, Bioinformatic SNP filter scripts |
Jeannine Peterson, Martin Schriefer, |
Magnolia: Microarray Data Management and Export System for PFGRC Microarrays |
Magnolia Application and Source Code |
|
Ginkgo: CGH and Expression Microarray Statistical Analysis and Normalization Platform |
Ginkgo Application and Source Code |
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Tutorial and Guide to Microarray Data Analysis: Image Analysis, Normalization and Data Mining |
Microarray Data Analysis Tutorial |