Fundamental patterns underlying gene expression profiles: simplicity from complexity.
Analysis of previously published sets of DNA microarray gene expression data by singular value decomposition has uncovered underlying patterns or "characteristic modes" in their temporal profiles. These patterns contribute unequally to the structure of the expression profiles. Moreover, the essential 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 fundamental patterns of gene expression change. These patterns are both simple and robust, dominating the alterations in expression of genes throughout the genome. Moreover, the characteristic modes of gene expression change in response to environmental perturbations are similar in such distant organisms as yeast and human cells. This analysis reveals simple regularities in the seemingly complex transcriptional transitions of diverse cells to new states, and these provide insights into the operation of the underlying genetic networks.
Holter
N S
NS
Department of Physics and Center for Materials Physics, 104 Davey Laboratory, Consortium, 519 Wartik Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
Mitra
M
M
Maritan
A
A
Cieplak
M
M
Banavar
J R
JR
Fedoroff
N V
NV
D018797:Cell Cycle Proteins / Q000235:genetics; D019204:GTP-Binding Proteins / Q000235:genetics; D020869:Gene Expression Profiling; D006801:Humans; D012441:Saccharomyces cerevisiae / Q000235:genetics
C082279:CDC15 protein; D018797:Cell Cycle Proteins; D019204:GTP-Binding Proteins