Gene expression temporal patterns

Microarray data cannot be analyzed by purely brute force techniques to generate a causal model of a set of biological processes because the data represents gene expression patterns that are only correlated with temporal processes of interest in the organism. Lander (1999) comments on this problem as follows ... 

Johnstone, I.L. and Barry, J.D. (1996) Temporal reiteration of a precise gene expression pattern during nematode development. EMBO Journal 15, 3633-3639. 

Roth A, Gill R, Certa U. 2003. Temporal and spatial gene expression patterns after experimental stroke in a rat model and characterization of PG4, a potential regulator of transcription. Mol Cell Neurosci 22 353. 

Doh, S.G., Vahlsing, H.L., Hartikka, J., Liang, X. and Manthorpe, M. (1997) Spatial-temporal patterns of gene expression in mouse skeletal muscle after injection of lacZ plasmid DNA. Gene Ther., 4, 648-663. 

Defining the spatial-temporal patterns of gene expression within cells/tissues. 

Cambell, S. J., Henderson, C. J., Anthony, D. C., Davidson, D., Clark, A. J., and Wolf, C. R. The murine CYP1A1 gene is expressed in a restricted special and temporal pattern during embryonic development. J. Biol. Chem. 280, 5828-5835, 2005. 

Church, M. J., Short, C. M., Jenkins, B. D., Karl, D. M., andZehr, J. P. (2005b). Temporal patterns of nitrogenase gene (niJEt) expression in the oligotrophic North Pacific Ocean. Appl. Environ. Microbiol. 71, 5362-5370. 

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