Gene expression measurement using cDNA and oligo arrays is exploding in popularity, yet many technical problems remain. One of the more challenging problems results from the large volume of data generated in these experiments. Image capture, processing, interpretation and quantification remain as important fundamental issues. Quality control and experimental design must be carefully addressed. Numerous statistical, image processing and bioinformatics issues remain problematic. Accordingly, this projects seeks to address such problems. Progress in FY2001: In a major NIH-wide project, we have installed a new database for storage, retrieval and analysis of Affymetrix oligo-based microarrays. Currently, three ICs, CC, NHLBI and NINDS are participating in this project . As part of this collaboration, we are creating a data analysis pipeline and bioinformatics toolset, including both commercial and freely available software. The database currently stores information from over 200 microarrays. We are also evaluating commercial software including OmniViz, PartekPro, Spotfire, Celera Discovery System, GeneSpring and others, for utility in developing this bioinformatics infrastructure. Working with laboratories in NCI, CC, NHLBI, NINDS, NIAID, NHGRI, NICHD, NIA, NIDDK, NIDA we have developed and applied software for the analysis of array images from major commercial sources as well as from custom arrays. In one major collaboration with the Laboratory of Molecular Pharmacology, NCI, we have applied the F-SCAN program for image-analysis of NCI-produced fluorescence-labeled microarrays. This study of p53-knockout cells, seeks to identify the effect of such knockouts and of treatment with an anti-cancer agent upon the gene-expression, in hopes of unraveling components of the signalling pathways involving the p53-gene. Working closely with NCI investigators, MSCL staff created new statistical procedures which allow for a global view of the multiple, complex effects being studied. More than one hundred genes have been identified as being significantly involved in the cells response pathways here. In a second major collaboration with the Laboratory of Molecular Immunology, NHLBI, results of a microarray study of the effect of Interleukin-2 (IL-2) on gene expression were studied in the context of genomic organization. Several interim findings are quite intriguing and awaiting confirmatory studies. In a third major collaboration with Critical Care Medicine Department, CC, we have assisted in the experimental design, data processing and performed statistical analysis of four major studies. One studies the effect of interferon gamma or glucocorticoids on gene expression of human lung cells, as means of better understanding the effects of these therapeutic agents. A second looks at the effects of endotoxin in humans upon expression in peripheral blood mononuclear cells as a means to study inflammation in vivo. A third uses a rat model of sepsis to potentially identify genes or gene products that may serve as targets for therapeutic agents in the future. MSCL staff participated in a nationwide collaboration to advance sepsis research, a topic of high interest to critical care medicine. The focus is on applying new microarray and genomic techniques to advance this research objective. The MSCL staff has been called upon to provide advice and guidance to several Institutes and Laboratories as they consider setting up microarray core facilities and bioinformatics centers. In particular, NHLBI, NICHD, NINDS, NIDA and NIDDK have requested and received extensive consultations in this area. MSCL staff also participate in the NIH-wide Biomedical Information Science and Technology Initiative (BISTI) Consortium serve as the focus of biomedical computing issues at the NIH
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