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Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data

Yvonne JK Edwards, Anna E Lobley, Melissa M Pentony and David T Jones*

Author Affiliations

Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK

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Genome Biology 2009, 10:R50  doi:10.1186/gb-2009-10-5-r50

Published: 11 May 2009

Additional files

Additional data file 1:

Figure S1 is a four part figure detailing the distributions of four properties, expression abundance, decay rate, and frequency of miRNA and ubiquitin target sites between disordered and ordered sequences. The plots are similar to those shown in Figure 1 but use alternative definitions of disorder and order to partition the data. Figure S2 is a plot of the occurrence of miRNA target sites as the amount of disorder increases. Figure S2a represents the occurrence of miRNA target sites in highly ordered and highly disordered sequences. Figure S2b represents the occurrence of miRNA target sites between ordered and disordered sequences and Figure S2c shows the occurrence of miRNA target sites as the amount of disorder increases. Figure S3 is a series of plots showing the frequency of sequences that are predicted to contain at least one ubiquitin target site. Figure S3a compares these frequencies between highly ordered and highly disordered sequences. Figure S3b is a similar plot between ordered and disordered sequences. Figure S3c is a bar plot of the frequency of ubiquitinated sequences in populations of disordered, ordered and all sequences as the amount of disorder increases. Figure S4 is a series of plots showing the frequency of predicted ubiquitin target sites in relation to varying amounts of disorder. Figure S4a is a bar plot of the frequency of ubiquitinated residues in highly disordered and highly ordered sequences. Figure S4b is a bar plot of the occurrence of ubiquitinated residues between ordered and disordered sequences. Figure S4c is a plot of the frequency of ubiquitinated residues in ordered, disordered and all sequences as the proportion of disordered residues increases. Figure S5a, b provides evidence that the predictions of ubiquitin target sites are independent of the proportion of lysine residues in the sequence despite the fact that both increase with the amount of disorder in the sequence. Figure S5a is a plot of the relationship between predicted ubiquitin target sites and occurrence of lysine residues with increasing amounts of disorder. Figure S5b shows the occurrence of predicted ubiquitin target sites normalized to the frequency of lysine residues as disorder increases. Figure S6 shows the distribution of transcript pair correlations obtained from the samples in the combined microarray studies. The distribution was used to empirically derive P-value cut-offs for significant correlation values. Figure S7 is a receiver operating characteristic (ROC) curve obtained using the ubiquitin site prediction algorithm on experimentally determined ubiquitin target sites.

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Additional data file 2:

Table S1 is a color coded listing of molecular function GO terms that are over-represented in clusters of disordered transcripts. Table S2 is a color coded listing of biological process GO terms that are over-represented in clusters of disordered transcripts. Tables S3a details the datasets used in the study and their composition when filtered for redundancy at 90% sequence identity. Table S3b lists the number of sequences that are classed as ordered and disordered when binned according to the amount of disorder present. Table S4 lists the ubiquitin target site predictions for the experimentally determined ligase target dataset.

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