Showing papers by "Carter Coberley published in 2004"

System and method for determining matching patterns within gene expression data

Abstract: A computer-based system and method are provided for retrieving information from a number of data sources on a computer network containing biological data. The network database is organized in a b-tree configuration having a plurality of sample nodes. Each sample node includes a curated data set of pre-formatted and pre-computed summary biological data obtained from at least one biological sample. The plurality of sample nodes are organized in a hierarchical arrangement according to clinical relevance. A set of attributes is assigned to each sample node to facilitate navigation through the database using a browser accessible through a graphical user interface. The set of attributes including at least one taxonomy designation selected from the group including tissues, diseases, medications and sample parameters. Search results that are produced include automated reports of the summary biological data stored in the sample nodes and custom reports generated using the summary biological data.

Impact on Genetic Networks in Human Macrophages by a CCR5 Strain of Human Immunodeficiency Virus Type 1

Abstract: Human immunodeficiency virus type 1 (HIV-1) impacts multiple lineages of hematopoietic cells, including lymphocytes and macrophages, either by direct infection or indirectly by perturbations of cell networks, leading to generalized immune deficiency. We designed a study to discover, in primary human macrophages, sentinel genetic targets that are impacted during replication over the course of 7 days by a CCR5-using virus. Expression of mRNA and proteins in virus- or mock-treated macrophages from multiple donors was evaluated. Hierarchical agglomerative cluster analysis grouped into distinct temporal expression patterns >900 known human genes that were induced or repressed at least fourfold by virus. Expression of more than one-third of the genes was induced rapidly by day 2 of infection, while other genes were induced at intermediate (day 4) or late (day 7) time points. More than 200 genes were expressed exclusively in either virus- or mock-treated macrophage cultures, independent of the donor, providing an unequivocal basis to distinguish an effect by virus. HIV-1 altered levels of mRNA and/or protein for diverse cellular programs in macrophages, including multiple genes that can contribute to a transition in the cell cycle from G(1) to G(2)/M, in contrast to expression in mock-treated macrophages of genes that maintain G(0)/G(1). Virus treatment activated mediators of cell cycling, including PP2A, which is impacted by Vpr, as well as GADD45 and BRCA1, potentially novel targets for HIV-1. The results identify interrelated programs conducive to optimal HIV-1 replication and expression of genes that can contribute to macrophage dysfunction.

Effects of Human Immunodeficiency Virus Type 1 Infection on CCR5 and CXCR4 Coreceptor Expression on CD4 T Lymphocyte Subsets in Infants and Adolescents

Abstract: HIV-1 infection alters expression of CCR5 and CXCR4 on CD4 T cells in adults, although an effect by virus on expression of coreceptor genes in pediatric subjects is unknown. We designed an exploratory study to evaluate surface expression of CXCR4 and CCR5 on CD45RA and CD45RO subsets of CD4 T lymphocytes from 17 HIV-1-infected infants and adolescents and 16 healthy age-matched individuals. While age in the absence of HIV-1 infection was unrelated to coreceptor expression, infection affected coreceptor expression differentially in infants and adolescents. Among infected adolescents, CCR5 and CXCR4 expression was significantly increased on CD4 CD45RO T cells, while CXCR4 was diminished in the CD4 CD45RA subset. Although HIV-1 infection in infants was also associated with increased CXCR4 expression on the CD4 CD45RO subset, in contrast to adolescents, infection in infants had no impact on coreceptor expression within the CD45RA CD4 subset. The proportion of CD4 T cells coexpressing CD45RA and CD45RO was increased by infection in both infants and adolescents. The CD45RA CD45RO subset in culture expressed high levels of CD4, CXCR4, and CD69, an early activation marker, and was highly susceptible to HIV-1 infection and replication. Infection of transitional CD4 T cells coexpressing CD45RA and CD45RO could contribute in part to provirus in either CD45RA or CD45RO subsets. Deleterious effects by HIV-1 infection on CD4 T cell homeostasis were greater in infants then adolescents, indicating that adolescence may be an optimal age group for assessing vaccines to prevent or treat HIV-1 infection.

Match/X, A gene expression pattern recognition algorithm used to identify genes which may be related to CDC2 function and cell cycle regulation.

Abstract: Large-scale microarray gene expression studies can provide insight into complex genetic networks and biological pathways. A comprehensive gene expression database was constructed using Affymetrix GeneChip microarrays and RNA isolated from more than 6,400 distinct normal and diseased human tissues. These individual patient samples were grouped into over 700 sample sets based on common tissue and disease morphologies, and each set contained averaged expression data for over 45,000 gene probe sets representing more than 33,000 known human genes. Sample sets were compared to each other in more than 750 normal vs. disease pairwise comparisons. Relative up or down-regulation patterns of genes across these pairwise comparisons provided unique expression fingerprints that could be compared and matched to a gene of interest using the Match/X algorithm. This algorithm uses the kappa statistic to compute correlations between genes and calculate a distance score between a gene of interest and all other genes in the d...