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1.
Figure 6

Figure 6. From: Upstream plasticity and downstream robustness in evolution of molecular networks.

The histogram of amino acid sequence identities (PID) of 2299 pairs of paralogous yeast proteins used in our study.

Sergei Maslov, et al. BMC Evol Biol. 2004;4:9-9.
2.
Figure 1

Figure 1. From: Upstream plasticity and downstream robustness in evolution of molecular networks.

The illustration of a concept of overlap in a molecular network. For a pair of paralogs the overlap Ω is defined as the number of their common neighbors in the network. In the case of a transcription network the (upstream) regulatory overlap Ωreg is given by the number of transcription factors regulating both paralogs, while for the physical interaction network the interaction overlap Ωint counts their common binding partners. The pair of paralogs used in this illustration has the overlap Ω = 2 out of the total of 5 distinct neighbors of the pair. That corresponds to a normalized overlap of 2/5 = 0.40.

Sergei Maslov, et al. BMC Evol Biol. 2004;4:9-9.
3.
Figure 4

Figure 4. From: Upstream plasticity and downstream robustness in evolution of molecular networks.

Protective effect of paralogs in a nematode worm C. elegans. The fraction of essential (non-viable RNAi phenotype [8]) proteins among all tested worm proteins as a function of PID to their most similar paralog in the worm genome. Note the apparent plateau between 70% and 100% PID. The plot in the inset shows the fraction of essential proteins among all RNAis tested in Ref. [8], while that in the main panel drops RNAis that are predicted [8] to target mRNA products of more than one gene. Note that while the graph in the main panel is qualitatively similar to that in Fig. 3B, in the inset the fraction of essential proteins at PID = 100% rises to its level for singleton proteins. Thus when mRNAs of highly similar paralogs are eliminated along with the targeted mRNA, the protective effect of paralogs totally disappears.

Sergei Maslov, et al. BMC Evol Biol. 2004;4:9-9.
4.
Figure 5

Figure 5. From: Upstream plasticity and downstream robustness in evolution of molecular networks.

Divergence of physical interaction neighborhoods of duplicated genes in a bacterium H. pylori and a fly D. melanogaster. The average value of the interaction overlap Ωint of paralogous proteins in H. pylori (A) and D. melanogaster (B) as a function of the amino acid sequence similarity. The physical interaction data are taken from Ref. [6] for H. pylori (A) and from Ref. [7] for D. melanogaster. Note the apparent plateau for PID's between 50% and 100% in panel A and its absence in panel B. Dashed horizontal lines show the average interaction overlap of a random (usually non-paralogous) pair of proteins. The solid line in B is the best fit to the exponential form: Ωint ~ exp(γFLYPID) with γfly = 0.045.

Sergei Maslov, et al. BMC Evol Biol. 2004;4:9-9.
5.
Figure 2

Figure 2. From: Upstream plasticity and downstream robustness in evolution of molecular networks.

Divergence of the upstream transcriptional regulation of duplicated genes in yeast. A) The distribution of the regulatory overlap Ωreg of paralo-gous proteins. The y-axis – Ωreg – is the number of transcription factors that cis-regulate both genes encoding a given pair of paralogous proteins. The x-axis is the percent identity (PID) of amino acid sequences of these two proteins. The colorbar shows the likelihood of finding a given Ωreg in a given 10% PID bin (note the logarithmic scale). The data describing the yeast regulatory network were taken from the whole genome chip-on-chip binding assay of 106 transcription factors [2], while the list of pairs of paralogous proteins was obtained by the whole genome blastp search (see Methods for more details.). B) The PID dependence of the average regulatory overlap Ωreg normalized by the total number of regulators of either one or the other paralog. Relative error bars are estimated by the inverse square root of the total number of shared regulators in a given PID bin. The solid line is the best fit to the exponential form: Ωreg ~ exp(γ PID) with γ = 0.03 (3% change in Ωreg for every 1% change in PID.) The dashed horizontal line at 0.015 is a null-model expectation of the normalized overlap of two randomly selected proteins (not necessarily paralogs).

Sergei Maslov, et al. BMC Evol Biol. 2004;4:9-9.
6.
Figure 3

Figure 3. From: Upstream plasticity and downstream robustness in evolution of molecular networks.

Divergence of downstream functions of duplicated genes in the baker's yeast S. cerevisiae. A. The average value of the interaction overlap Ωint – the number of physical interaction partners shared by a pair of paralo-gous proteins – as a function of the similarity of their amino acid sequences. The physical interaction data are taken from the set of Uetz et al. [3] (open circles), the core dataset of Ito et al. [4] (diamonds), and the non-redundant combination of the two (filled circles). Note the apparent plateau for PID's between 70% and 100% in all three datasets. Solid lines are guides for the eye. A randomly selected (usually non-paralogous) pair of proteins in the combined dataset on average has Ωint around 8 × 10-3 (off-limits in this figure). All data points at all PIDs are significantly above this null-model value. B. The fraction of essential (lethal null-mutant) proteins among all proteins tested in Ref. [5] as a function of PID to their most similar paralog in the yeast genome. Proteins with no paralogs (singletons) are binned at 0% PID. Note the apparent plateau between 50% and 100% PID. The inset (note the change of scale on the y-axis) shows the fraction of essential proteins in the subset of all proteins known to be localized in the yeast nucleus [17]. Here the effect becomes even more pronounced so that all 18 nuclear proteins protected by a paralog with at least 50% similarity were found to be non-essential.

Sergei Maslov, et al. BMC Evol Biol. 2004;4:9-9.

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