Fundamental patterns underlying gene expression profiles: Simplicity from complexity

Analysis of previously published sets of DNA microarray gene expression dat a by singular value decomposition has uncovered underlying patterns or "cha racteristic modes" in their temporal profiles. These patterns contribute un equally to the structure of the expression profiles. Moreover, the essentia l features of a given set of expression profiles are captured using just a small number of characteristic modes. This leads to the striking conclusion that the transcriptional response of a genome is orchestrated in a few fun damental patterns of gene expression change. These patterns are both simple and robust, dominating the alterations in expression of genes throughout t he genome. Moreover, the characteristic: modes of gene expression change in response to environmental perturbations are similar in such distant organi sms as yeast and human cells. This analysis reveals simple regularities in the seemingly complex transcriptional transitions of diverse cells to new s tates, and these provide insights into the operation of the underlying gene tic networks.