GO for integration of expression data.

The low reproducibility of differential expression of individual genes in microarray experiments has led to the suggestion that experiments be analyzed in terms of gene characteristics, such as GO categories or pathways, in order to enhance the robustness of the results. An implicit assumption of this approach is that the different experiments in effect randomly sample the genes participating in an active process. We argue that by the same rationale it is possible to perform this higher-level analysis on the aggregation of genes that are differentially-expressed in different expression-based studies, even if the experiments used different platforms. The aggregation increases the reliability of the results, it has the potential for uncovering signals that are liable to escape detection in the individual experiments, and it enables a more thorough mining of the ever more plentiful microarray data. We present here a proof-of-concept study of these ideas, using ten studies describing the changes in expression profiles of human host genes in response to infection by Retroviridae or Herpesviridae viral families. We supply a tool (accessible at www.cs.bgu.ac.il/∼waytogo) which enables the user to learn about genes and processes of interest in this study.

African descents are more sensitive than European descents to the antitumor compounds α-hederin and kalopanaxsaponin I.

α-Hederin, a natural triterpene saponin and its derivative kalopanaxsaponin I (ksI) exhibit cytotoxicity against various cancer cell lines and IN VIVO tumors. We studied the genetic variants contributing to the activity of these two anticancer compounds. Cell lines derived from 30 trios of European descent (Centre d'Etude du Polymorphisme Human, CEPH; CEU) and 30 trios of African descent (Yoruban, YRI) were used. Cytotoxicity was determined as inhibition of cell growth at increasing concentrations of α-hederin or ksI for 24 h. In comparison to the European, the Yoruban populations revealed a higher sensitivity to α-hederin and to ksI that can be attributed to several unique SNPs. These SNPs are located near 111 and 130 genes in the European and the Yoruban populations, respectively, raising the possibility that some of these genes contribute to the differential sensitivity to these compounds.