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. 2000 Jul 18;97(15):8409-14.
doi: 10.1073/pnas.150242097.

Fundamental patterns underlying gene expression profiles: simplicity from complexity

N S Holter  1 , M Mitra, A Maritan, M Cieplak, J R Banavar, N V Fedoroff
Affiliations

Fundamental patterns underlying gene expression profiles: simplicity from complexity

N S Holter et al. Proc Natl Acad Sci U S A. .

Abstract

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.

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Figures

Figure 1
Figure 1
Characteristic modes (Xi(t)) for the gene expression and random data sets. (a) Yeast cell cycle data (3). The circles correspond to the 15 time-point series, and the squares in the first five panels correspond to a truncated time series with only 12 time points. The bottom panel is an overlay of modes 6–15 for the 15 time-point series only. (b) Yeast sporulation data (5). The circles correspond to modes generated from sporulation specific genes whereas the squares correspond to modes generated from genes in the complete data set (entire yeast genome). (c) Human fibroblast data (4). The format is the same as in a, except that the bottom panel is an overlay of modes 6–12. (d) Random data with the same number of genes and time points as the sporulation data.
Figure 2
Figure 2
A reconstruction of the expression profiles for the yeast cell cycle data set from the characteristic modes. Panels 1–5 show the results of a hierarchical reconstruction of the expression profiles using only the first 1, 2, 3, 4, and 5 characteristic modes. The last panel uses all 14 characteristic modes and exactly reproduces the original data set. Each row in each of the panels represents a different gene, and each column represents a different time point. The gray scale ranges from white (maximal expression) to black (minimal expression). The genes are ordered as in ref. .
Figure 3
Figure 3
A reconstruction of the expression profiles for the yeast sporulation data set from the characteristic modes. The format is the same as in Fig. 2. The last panel uses all six characteristic modes and exactly reproduces the original data set. The genes are ordered as in ref. .
Figure 4
Figure 4
A reconstruction of the expression profiles for the human fibroblast data set from the characteristic modes. The format is the same as in Fig. 2. The last panel uses all 12 characteristic modes and exactly reproduces the original data set. The genes are ordered as in ref. .
Figure 5
Figure 5
Plot of the coefficients for characteristic mode 1 against the coefficients for characteristic mode 2. Symbols of different colors and shapes are used for genes that belong to the different clusters identified by the original authors (–5). (a) cdc15 data (first 12 time points). (b) Sporulation data (7 time points). (c) Fibroblast data (13 time points). (d) random data (7 time points).
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References

    1. Pease A C, Solas D, Sullivan E J, Cronin M T, Holmes C P, Fodor S P. Proc Natl Acad Sci USA. 1994;91:5022–5026. - PMC - PubMed
    1. Schena M, Shalon D, Davis R W, Brown P O. Science. 1995;270:467–470. - PubMed
    1. Spellman P T, Sherlock G, Zhang M Q, Iyer V R, Anders K, Eisen M B, Brown P O, Botstein D, Futcher B. Mol Biol Cell. 1998;9:3273–3297. - PMC - PubMed
    1. Iyer V R, Eisen M B, Ross D T, Schuler G, Moore T, Lee J C F, Trent J M, Staudt L M, Hudson J, Jr, Boguski M S, et al. Science. 1999;283:83–87. - PubMed
    1. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown P O, Herskowitz I. Science. 1998;282:699–705. - PubMed

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