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Component 4 of the BayGenomics project is led by Dr. Bruce Conklin, an Assistant Professor of Medicine and Pharmacology at UCSF and Assistant Investigator at Gladstone. The goal of Component 4 is to produce custom microarrays containing thousands of mouse genes, including those inactivated within the gene-trap resource. These microarrays are being used in gene-profiling experiments to identify genes that are expressed at high levels in the heart and lung, to identify genes that are differentially expressed in model cardiopulmonary diseases, and to analyze physiologic perturbations in knockout mice. More information about our expression microarray technology is available from the Gladstone Genomics Core.
The Gladstone Genomics Core is now producing DNA microarrays containing 70-mer oligonucleotides. Available array project descriptions and data include:
- Hybridization Reproducibility
- DO11.1 Stimulation with PMA/Ionomycin
- Effect of processing DO11.1 cells through cell sorter
- Microarray data of murine asthma and pulmonary fibrosis models
The size and complexity of gene-profiling data sets require custom databases and software analysis programs. Working closely with Component 2 investigators, the personnel within Component 4 are assigning each gene to a predicted functional group, and when possible, to a cellular pathway. This functional information is incorporated into GenMAPP, a new software program that allows investigators to automatically map data from gene-profiling experiments onto known biochemical pathways.
GenMAPP (Gene MicroArray Pathway Profiler) is a free computer application designed to visualize gene expression data on MAPPs representing biological pathways and groupings of genes. A MAPP is a special file format produced by GenMAPP that shows the biological relationship between genes or gene products. GenMAPP has graphics tools that can be used to draw MAPPs according to any organizing principle such as metabolic pathways, signal transduction cascades, subcellular locations, or gene families. GenMAPP then automatically links each gene on a MAPP to data from gene expression experiments imported by the user. The user may then set criteria to dynamically view those data on a MAPP. For example, the user can tell GenMAPP to color all genes up-regulated in an experiment red and color all genes down-regulated in an experiment blue. Since genes are colored and viewed dynamically, the user can easily switch criteria to see what genes change with different fold cut-offs, for example. The GenMAPP program also provides basic annotation for each gene on a MAPP from the GenBank and SwissProt public databases, including hyperlinks to each gene's entry in those databases. Currently, the GenMAPP program is packaged with a combined mouse and human gene database containing over 130,000 gene accession numbers. The GenMAPP program, a growing collection of MAPPs, and gene databases for other model organisms can be downloaded from www.GenMAPP.org.
Several significant improvements have been made to GenMAPP in 2001. The number of publicly distributed MAPPs has increased from 60 in April 2001 to over 600 in October 2001. The database that allows GenMAPP to work has also been improved with 100,000 gene entries in April 2001 to over 130,000 genes with the September 2001 update. GenMAPP was also featured in the new products section of Science in October 2001.
Further information on gene trapping technology is available from www.genetrap.org.