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

Agency
National Institute of Health (NIH)
Institute
Center for Information Technology (CIT)
Type
Intramural Research (Z01)
Project #
1Z01CT000266-04
Application #
6540965
Study Section
(MSCL)
Project Start
Project End
Budget Start
Budget End
Support Year
4
Fiscal Year
2001
Total Cost
Indirect Cost
Name
Computer Research and Technology
Department
Type
DUNS #
City
State
Country
United States
Zip Code
Deans, Katherine J; Minneci, Peter C; Chen, Hao et al. (2009) Impact of animal strain on gene expression in a rat model of acute cardiac rejection. BMC Genomics 10:280
Raghavachari, Nalini; Xu, Xiuli; Munson, Peter J et al. (2009) Characterization of whole blood gene expression profiles as a sequel to globin mRNA reduction in patients with sickle cell disease. PLoS One 4:e6484
Greenwell-Wild, Teresa; Vazquez, Nancy; Jin, Wenwen et al. (2009) Interleukin-27 inhibition of HIV-1 involves an intermediate induction of type I interferon. Blood 114:1864-74
Nares, Salvador; Moutsopoulos, Niki M; Angelov, Nikola et al. (2009) Rapid myeloid cell transcriptional and proteomic responses to periodontopathogenic Porphyromonas gingivalis. Am J Pathol 174:1400-14
Raat, Nicolaas J H; Noguchi, Audrey C; Liu, Virginia B et al. (2009) Dietary nitrate and nitrite modulate blood and organ nitrite and the cellular ischemic stress response. Free Radic Biol Med 47:510-7
Woszczek, Grzegorz; Chen, Li-Yuan; Nagineni, Sahrudaya et al. (2008) Leukotriene D(4) induces gene expression in human monocytes through cysteinyl leukotriene type I receptor. J Allergy Clin Immunol 121:215-221.e1
Hernandez-Novoa, Beatriz; Bishop, Lisa; Logun, Carolea et al. (2008) Immune responses to Pneumocystis murina are robust in healthy mice but largely absent in CD40 ligand-deficient mice. J Leukoc Biol 84:420-30
Coppey, Mathieu; Boettiger, Alistair N; Berezhkovskii, Alexander M et al. (2008) Nuclear trapping shapes the terminal gradient in the Drosophila embryo. Curr Biol 18:915-9
Raghavachari, Nalini; Xu, Xiuli; Harris, Amy et al. (2007) Amplified expression profiling of platelet transcriptome reveals changes in arginine metabolic pathways in patients with sickle cell disease. Circulation 115:1551-62
Elshal, Mohamed F; Khan, Sameena S; Raghavachari, Nalini et al. (2007) A unique population of effector memory lymphocytes identified by CD146 having a distinct immunophenotypic and genomic profile. BMC Immunol 8:29

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