Additional file 3: Table S1. of Characterisation of the global transcriptional response to heat shock and the impact of individual genetic variation

Differentially expressed genes following heat shock. Differentially expressed genes for a panel of 43 LCLs exposed to heat shock (42 °C for 1 h, 6 h recovery) and assayed by microarray are shown following limma analysis (FC >1.2, FDR <0.01). Table S2. GO categories enriched for upregulated genes. GO categories for differentially expressed genes upregulated following heat shock in LCLs are shown. Numbers of significant and expected genes shown, together with p values (Fisher’s exact test). Table S3. GO categories enriched for downregulated genes. GO categories for differentially expressed genes downregulated following heat shock in LCLs are shown. Numbers of significant and expected genes shown, together with p values (Fisher’s exact test). Table S4. Network analysis following heat shock. Networks identified on IPA analysis of differentially expressed genes (FC >1.2, FDR <0.01) following heat shock. Table S5. Genes with newly established links to heat shock response. Genes listed together with FC and FDR following heat shock, and p value for presence of the heat shock binding motif. Table S6. Summary of HSF-binding evidence for the promoters of novel and established heat shock response genes. Presence of ChIP-seq peak for HSF1 or HSF2 and HSF1 motif indicated in relation to heat shock genes. Table S7. Differential gene expression between PLS clusters. Differential gene expression between samples assigned to PLS cluster 1 and 2 as assessed by limma analysis is shown for all assayed probes. Table S8. GO categories enriched for genes with increased expression in cluster 2. GO categories for genes differentially expressed between PLS clusters. Categories enriched for genes with increased expression in cluster 2 are shown. Numbers of significant and expected genes shown, together with p values (Fisher’s exact test). Table S9. GO categories enriched for genes with increased expression in cluster 1. GO categories for genes differentially expressed between PLS clusters. Categories enriched for genes with increased expression in cluster 1 are shown. Numbers of significant and expected genes shown, together with p values (Fisher’s exact test). (XLSX 4875 kb

Additional file 1: Figure S1. of Characterisation of the global transcriptional response to heat shock and the impact of individual genetic variation

PCA plot of ComBat corrected gene expression. PCA plot for gene expression in LCLs following heat shock post microarray processing and QC with individual lines coloured by BeadChIP. (PDF 166 kb

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

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

Functional description of co-expressed cluster genes.

<p>Functional gene descriptions and positions of over-represented promoter motifs on predicted clusters and neighboring genes. Expression of genes is illustrated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110311#pone-0110311-g002" target="_blank">Figure 2</a>.</p><p>Functional description of co-expressed cluster genes.</p

Used gene expression experiments.

<p>Overview of used gene expression experiments, data obtained from PlexDB <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110311#pone.0110311-Dash1" target="_blank">[37]</a>.</p><p>Used gene expression experiments.</p

Functional description of cluster genes with correlated expression pattern.

<p>Functional gene descriptions of predicted clusters C16 and C64 illustrated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110311#pone-0110311-g003" target="_blank">Figure 3</a>.</p><p>Functional description of cluster genes with correlated expression pattern.</p

Functional description of genes with putative HGT.

<p>Functional gene descriptions and positions of over-represented promoter motifs on predicted clusters and neighboring genes. Orthologs of the predicted clusters are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110311#pone-0110311-g004" target="_blank">Figures 4</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110311#pone-0110311-g005" target="_blank">5</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110311#pone-0110311-g006" target="_blank">6</a>.</p><p>Functional description of genes with putative HGT.</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

Evidence of horizontal gene transfer and regulation of predicted C47 cluster.

<p>(A) Predicted gene cluster in <i>Fusarium graminearum</i> and orthologous genes in <i>F. pseudograminearum</i> and the <i>Botrytis fuckeliana</i> strains B05.01 and T4 (solid dark blue arrows) on their respective supercontigs (light blue boxes). Adjacent genes are illustrated as white arrows, dashed lines depict orthologous groups. The gypsy transposable element in <i>B. fuckeliana</i> B05.01 is indicated as orange box. 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>. (B) The heatmap illustrates fold changes in gene expression (log2 scale) between two 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. (C) Histograms show whole genome distributions of open reading frame GC ratios in <i>F. graminearum</i> (blue) and <i>B. fuckeliana</i> B05.01 (red). Vertical lines illustrate GC ratios of cluster genes.</p