Performance comparison of SENNA with common SRL programs and syntactic parsers.

<p>Performance time (ptime) of SENNA* (the SENNA variant we used for PAS generation), ASSERT and Stanford PCFG and lexicalized parser were measured relative to SENNA 1.0 web version on four test sets of 500 sentences each. The length interval of the sentences ranged from 65–75 characters for the first test set to 235–245 characters in the fourth test set. The Enju-mogura parser appeared to have difficulties specifically with the 175 character test set we used, processing times on other sentences of similar sentence length resulted in processing times comparable to the mogura results on the 65, 135 and 235 characters test sets.</p

Determination of the average sentence length in the test sets as well as in the three sources of biomedical literature used for PAS extraction.

<p>Evaluation of average sentence length in characters for different literature resources in the biomedical domain.</p>*)<p>including titles.</p>**)<p>excluding titles.</p

Evaluation of SENNA* on LLL'05 and BC-PPI corpus.

<p>Precision and recall of RE step applied on the LLL'05 and BC-PPI data set. All TPs, FPs and FN in both data sets were summed up for an overall value for precision, recall and F-measure.</p

Histogram of the fraction of wrongly predicted verbs covering the 5000 most frequent verb-candidates.

<p>After checking those 5000 verb-candidates manually for false verb assignments, the candidates were grouped in 100 subsets of 50 verb-candidates. For each group the fraction of verb-candidates wrongly labeled as “verb” by SENNA was evaluated (y-axis). The histogram shows these 100 subsets ordered by descending candidate – frequency from left to right. With decreasing term frequency, the number of wrong assignment rises.</p

DEXP Values for S/MAR− Genes and as a Function of the Position of the S/MAR within S/MAR+ Genes

<p>The 5% confidence intervals are shown.</p

Median Expression Values of S/MAR− and S/MAR+ Genes in Different Organs, Root Tissues, and Flower Tissues

<p>MPSS data recorded in five different organs are shown (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 1) (A); for Affymetrix-based measurements (B–D), median values for five root tissues (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 2) (B), ten organs (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 4) (C), and five flower tissues (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 6) (D) are given. For MPSS-based experiments (A), tpm are indicated; for experiments based on the Affymetrix platform (B–D), Affymetrix expression values are plotted. The 5% confidence intervals calculated using bootstrap set for all values are shown.</p

DEXP Values for S/MAR+ and S/MAR− TF Genes for Different Datasets

<p>The 5% confidence intervals for all values are shown.</p

Orthologous genes and regulation of predicted C62 cluster.

<p>(A) Predicted gene cluster in <i>Fusarium graminearum</i> and orthologous genes in <i>F. pseudograminearum</i>, <i>Cochliobolus heterostrophus</i> and <i>Pyrenophora teres</i>. (solid dark blue arrows) on their respective supercontigs (light blue boxes). Adjacent genes are shown in white, dashed lines between genes illustrate orthologous groups. Enumeration in <i>F. graminearum</i> is according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110311#pone-0110311-t005" target="_blank">Table 5</a>. Reverse transcriptase in <i>C. heterostrophus</i> is indicated as “RT”. (B) Heatmap illustrates fold changes in gene expression (log2 scale) of cluster and adjacent genes between experimental conditions. Genes are listed in chromosomal order on y-axis. Horizontal grey bars show boundaries of predicted clusters. Abbreviations of experimental conditions on x-axis are according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110311#pone-0110311-t006" target="_blank">Table 6</a>. No expression data is available for FGSG_17401, as a distinct mapping of probes on this gene model was not possible.</p

Differential gene expression heatmap of clusters and neighboring genes.

<p>Heatmaps illustrate fold changes in gene expression (log2 scale) between experimental conditions. Genes are listed in chromosomal order on y-axis. Abbreviations of experimental conditions on x-axis are according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110311#pone-0110311-t006" target="_blank">Table 6</a>. Horizontal grey bars show boundaries of predicted clusters.</p

Secondary metabolites produced by <i>F. graminearum</i> and corresponding biosynthetic genes or gene clusters.

<p>Currently known secondary metabolites of <i>F. graminearum</i> and corresponding genes (gene clusters) required for biosynthesis. PKS: Polyketide synthases, NPS: Non-ribosomal peptide synthetase, TPS: Terpenoid synthases, CYP: Cytochrome P450.</p><p>Secondary metabolites produced by <i>F. graminearum</i> and corresponding biosynthetic genes or gene clusters.</p