The mean absolute errors (MAE) of the 5 methods for different values of .

<p>The error bar at each data point is the standard error of MAE based on <i>in silico</i> experiments. Genes are assumed to be independent of each other. Overall the results here show that the most accurate method is ZG04 which has significantly lower MAE than the other methods for a wide range of values of . This figure also shows that ZG04, ST03 and Ch04 are much more stable than PM03 and PC04 whose MAEs fluctuate with changing .</p

The PM03 method becomes more accurate in a small strip of the parameter space around and .

<p>This figure shows that ZG04 is still the second most accurate method in this narrow strip.</p

Neighbor-Joining phylogenetic tree of the SBP domains of <i>Arabidopsis</i> and castor bean (A) and the corresponding gene structure analyses (B).

<p>Green boxes indicate the exon regions and lines indicate introns. The length of the boxes and lines are scaled based on the length of genes.</p

Summary of information on the SPL genes identified in castor bean.

a<p>The length indicates the protein length of each gene.</p

Genome-Wide Identification and Evolutionary Analysis of the SBP-Box Gene Family in Castor Bean

<div><p>Genes in the SQUAMOSA promoter-binding-protein (SBP-box) gene family encode transcriptional regulators and perform a variety of regulatory functions that involved in the developmental and physiological processes of plants. In this study, a comprehensive computational analysis identified 15 candidates of the SBP-box gene family in the castor bean (<i>Ricinus communis</i>). The phylogenetic and domain analysis indicated that these genes were divided into two groups (group I and II). The group II was a big branch and was further classified into three subgroups (subgroup II-1 to 3) based on the phylogeny, gene structures and conserved motifs. It was observed that the genes of subgroup II-1 had distinct evolutionary features from those of the other two subgroups, however, were more similar to those of group I. Therefore, we inferred that group I and subgroup II-1 might retain ancient signals, whereas the subgroup II-2 and 3 exhibited the divergence during evolutionary process. Estimation of evolutionary parameters (d_N and d_N/d_S) further supported our hypothesis. At first, the group I was more constrained by strong purifying selection and evolved slowly with a lower substitution rate than group II. As regards the three subgroups, subgroup II-1 had the lowest rate of substitution and was under strong purifying selection. By contrast, subgroups II-2 and 3 evolved more rapidly and experienced less purifying selection. These results indicated that the different evolutionary rates and selection strength caused the different evolutionary patterns of the members of SBP-box genes in castor bean. Taken together, these results provide better insights into understanding evolutionary divergence of the members of SBP-box gene family in castor bean and provide a guide for future functional diverse analyses of this gene family.</p></div

Comparison of the mean d_N value for two groups (A) and three subgroups (B).

<p>Error bars indicate the standard error of the mean.</p

Additional file 1 of A gene-signature progression approach to identifying candidate small-molecule cancer therapeutics with connectivity mapping

Significant genes associated with HDAC inhibitors. The full list of 104 genes (probesets) and their rank order, obtained in the “simulated experiment” with 4 HDAC inhibitors of the CMap reference profiles. (TAB 6.85 kb