The local neighbourhood for the predicted virulence gene FGSG_06878.

<p>The neighbourhood of FGSG_06878 (prediction -large white triangle) and these 8 seed proteins to which it is linked, visualised with Ondex <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067926#pone.0067926-Kohler1" target="_blank">[16]</a>. The magenta coloured edges predicted PPI information, blue edges predicted co-expression information and the green coloured edges predict sequence similarity information.</p

Position of the predictions in relation to the 4 chromosomes of <i>Fusarium graminearum</i>.

<p>The predicted virulence genes are shown as black vertical bars in track 1 for each chromosome. The verified virulence seeds (red bars) are depicted in track 2. Recombination frequency across the chromosomes is depicted in track 3 using a colour gradient (white (0.0) lowest to crimson (>8 cM highest). The various colours in track 3 for each chromosome indicate the frequence of recombination (cM/27 kb), i. e. # clBeige 1 clKhaki 2 clGold 3 clGoldenRod 4 clTomato 8 clCrimson. The numbers between the colours are boundary values in cM/27 kb. Beige represents the lowest and crimson the highest recombination frequency <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067926#pone.0067926-Gale1" target="_blank">[47]</a>. (Image generated using OmniMapFree <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067926#pone.0067926-Antoniw1" target="_blank">[27]</a>).</p

Predicting virulence nodes based on the seed numbers connected within the local neighbourhood.

<p>The number of seeds to which each predicted virulence node is connected, in the four networks is shown. A node linked to 2 or more seed nodes is termed a prediction. Some predictions have links to multiple seeds.</p

Heat map displaying the taxonomic distribution for each of the predicted virulence associated proteins.

<p>Each row provides the information for one sequence. The left hand three columns (SEQ, PPI, COEX) indicate the network in which the prediction could be made (black). For the bottom 15 rows only the integrated network provides the prediction. The right hand heatmap shows the proportional distribution of all BLAST hits from the 215 predictions to the NCBI nr database (white – lowest, red - highest) across the taxonomical levels. All hits were counted once, at the lowest possible level of taxonomical specificity. The grey colour shows cases where there were no hits at a particular taxonomic level. See <b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067926#pone.0067926.s008" target="_blank">Table S2</a></b> for the detailed results for each individual FGSG protein.</p

The local neighbourhood for the predicted virulence gene FGSG_00071 <i>(TRI1)</i>.

<p>Gene IDs are: FGSG_03543 <i>(TRI14)</i>, FGSG_10397 <i>(CLM1)</i>, FGSG_17598 (related to O-methyl sterigmatocystin oxidoreductase), FGSG_03535 <i>(TRI4)</i>, FGSG_03534 <i>(TRI3)</i>, FGSG_16251 <i>(TRI6)</i>, FGSG_03540 <i>(TRI11).</i></p

The prediction of FGSG_06878 as a virulence factor with links to 8 seeds.

<p>This prediction FGSG_06878 was confirmed to be a virulence protein in the recent paper of [21-Wang et al.]. Note that prediction FGSG_06878 is linked to seed FGSG_06385 by both predicted PPI and sequence similarity information. In planta phenotypes are rv, reduced virulence, a quantitative reduction in disease causing ability and the more stringent lp, indicating loss of pathogenicity where disease establishment is aborted.</p

The neighbourhood of FGSG_05535 and FGSG_09988.

<p>Although connected to the two seed proteins FGSG_09614 <i>(GPA2)</i> and FGSG_04104 <i>(GPB1),</i> experimental evidence in barley suggests that the two predictions 05535 and 09988 are dispensable for pathogenicity <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067926#pone.0067926-Yu1" target="_blank">[36]</a>. Genetic redundancy is suggested to explain this fact. (FGSG_05698: probable <i>CPC2</i> protein, FGSG_09870: probable <i>CPC2</i> protein; FGSG_09271: probable <i>SEC13</i> - protein transport protein; FGSG_10251: probable <i>LST8</i> protein; FGSG_04618: related to vegetatible incompatibility protein <i>HET-E-1</i>; FGSG_16028: probable U5 snRNP-specific 40 kD protein (novel WD-40 repeat protein); FGSG_05038: probable nuclear migration protein.</p

The probability that a verified virulence (VV)seed is connected to at least 2 others by chance.

<p>The probability that a verified virulence (VV)seed is connected to at least 2 others by chance.</p

Comparison of the global properties of the four predicted networks.

<p>Global properties of the three constituent networks and the integrated network. The sequence similarity network excludes nodes with no edges (‘orphan’ proteins with no sequence similarity matches). Column 4 is the number of verified virulence (VV) seeds involved in the predictions, using the rule that a node must be connected to at least 2 seeds to be a prediction (in brackets are the corresponding numbers if we require connection to at least 3 seeds); Column 8 gives the number of predictions (in brackets are the corresponding prediction counts if we require a more stringent rule i. e. a node must be connected to at least 3 seeds to be a prediction).</p

Comparison of the distribution of known phenotypes of the seeds within the four predicted networks.

<p>Counts of the different phenotypes according to the study by Wang and collegues <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067926#pone.0067926-Wang1" target="_blank">[26]</a> that were found among the predictions derived using four different networks.</p