Clustering of gene expression patterns.

<p>(A) Bootstrap analysis of regularized-log transformed counts to assign confidence levels to sample clustering. Red values are approximately unbiased p values and green values are bootstrap probabilities. Red boxes indicate clusters supported at a confidence level of 99%. (B) Principal component analysis of regularized-log transformed counts of differentially expressed genes. Black spheres represent unaffected bats and white spheres represent WNS-affected bats.</p

Hierarchical clustering of gene expression in WNS-affected and unaffected bats.

<p>Hierarchical clustering of differentially expressed genes using Pearson correlation complete-linkage clustering. Scale shows Pearson correlation coefficient.</p

REVIGO treemap summarizing gene ontology biological process categories over-represented in WNS-affected tissues.

<p>GOrilla was used to identify Gene Ontology Biological Processes that were over-represented among transcripts more highly expressed in WNS-affected tissues at an FDR cutoff of 0.1 (<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005168#ppat.1005168.s008" target="_blank">S6 Table</a>). Over-represented categories with p values of less than 0.001 (290 terms) were used to generate a treemap colored by functional category. The size of each rectangle is proportional to the p value for that category.</p

Selected over-represented gene ontology biological process categories.

<p>¹ Over-represented p value.</p><p>² False discovery rate after Benjamini-Hochberg adjustment for multiple comparisons.</p><p>³ Enrichment of differentially expressed genes in this category.</p><p>⁴ Number of differentially expressed genes in this category identified by GOrilla at a p value cutoff of 0.001.</p><p>⁵ Number of genes in this GO category represented in the background set.</p><p>Selected over-represented gene ontology biological process categories.</p

Global transcriptional analysis of WNS-affected and unaffected bats by RNA-Seq.

<p>Centered log₂ fold changes are shown for the 100 most significant differentially expressed identified genes. Adjusted p values ranged from 3.3x10^-5 to 2.8x10^-18. The heatmap of TMM-normalized FPKM expression estimates is centered and log₂ scaled from a minimum of -4.8 to a maximum of 4.8. Transcripts were identified by BLAST alignment to the SwissProt database.</p

Selected genes differentially expressed in WNS-affected tissues.

<p>¹ BLAST hit with the lowest E-value in the Swissprot database. Only genes with E < 1E-05 were considered.</p><p>² Fold change in gene expression of the WNS-affected samples compared to the unaffected samples as determined by DESeq2. Negative values indicate higher expression in the unaffected samples.</p><p>³ Probability of differential expression determined by DESeq2.</p><p>⁴ Adjusted probability of differential expression after Benjamini-Hochberg FDR correction.</p><p>⁵ Posterior probability fold change in EBSeq-estimated expression of each transcript in WNS-affected tissues over unaffected tissues. NA indicates that no isoform for that gene was differentially expressed at an FDR < 0.001</p><p>⁶ Posterior probability estimate by EBSeq that the isoform is differentially expressed.</p><p>Selected genes differentially expressed in WNS-affected tissues.</p

Expression of destructin transcripts in <i>Pd</i> growing on WNS-affected bats.

<p>¹ Trimmed mean of M-values- (TMM-) normalized expression determined by RSEM in fragments per kilobase of transcript per million mapped reads (FPKM).</p><p>Expression of destructin transcripts in <i>Pd</i> growing on WNS-affected bats.</p

Hierarchical clustering of <i>Pd</i> gene expression on bats with WNS.

<p>Hierarchical clustering of differentially expressed Pd genes using Pearson correlation complete-linkage clustering. Scale shows Pearson correlation coefficient.</p