The “<i>resistance</i>” class.

<p>The “<i>resistance</i>” class has been opened to show the different contents. The black boxes denote an “<i>agent_in</i>” relation.</p

The “<i>biological material</i>” class.

<p>The figure shows, in a depth of 5 levels, the class “biological material” (A) and, within the “<i>Cellia</i>” subgenus, the <i>Anopheles gambiae</i> s.s.-related terms (B), that also include the chromosomal and molecular forms.</p

The IRbase schema.

<p>The figure shows the different tables that make up the schema. 1 and * denote a “one to many” relationship.</p

The upper levels of the MIRO.

<p>The figure shows the upper levels of the ontology. The small circles denote an “<i>is_a</i>” relation between the term and its parent, and small rectangles show the presence (plus) or absence (minus) of children for a given term. The children of the four “<i>biological material</i>”, “<i>insecticidal substance</i>”, “<i>method</i>” and “<i>resistance</i>” are shown in a depth of 2 levels. The “<i>gazetteer</i>” class has been loaded into MIRO (see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0000465#s3" target="_blank">Results and Discussion</a>) and is therefore visible here.</p

Summary of the genes differentially transcribed between resistant and susceptible strains.

<p>The Venn diagram shows the number of genes found significantly (P value<0.01) over- or under-transcribed (>2 fold in either direction) in one or both resistant strains compared to the susceptible New Orleans strain. Upward arrows indicate over- transcribed in resistant strains, downward represent under-transcribed.</p

Quantitative PCR analysis of selected genes from the microarray experiments.

<p>Relative-fold change in transcript and gene copy number normalised to two ribosomal genes was compared between the resistant CAYMAN (A) and CUBA-DELTA (B) strains against the NEW ORLEANS susceptible strain. Transcript levels are shown by the white columns and gene copy numbers by the grey columns. Error bars represent 95% confidence intervals.</p

GO term enrichment analysis.

<p>The analysis was performed on the significantly up-regulated genes found in CAYMAN and CUBA-DELTA compared to NO. The BLAST2GO software was used for the annotation, mapping and enrichment analysis. The figure represents all the significant GO-term categories found significantly enriched compared to the reference set (all transcripts present on the microarray) after a Fisher's exact test and Benjamini and Hochberg multiple testing correction (Pval<0.05). The test set percentage indicates the percentage of up regulated genes belonging to a GO term category compared to all up-regulated genes used in the GO-term analysis while the reference set percentage indicates the percentage of a particular GO-term category compared to all genes with GO-terms on the microarray.</p

Accession numbers and putative functions for the 20 genes showing the highest elevation in expression in the CAYMAN vs NO comparison and the 20 genes showing the highest decrease in expression in the same comparison.

<p>Detoxification genes are shown in bold.</p

Unrooted distance neighbour joining tree showing phylogeny of <i>Aedes aegypti</i> CYP9 genes.

<p>Nodes with >70% bootstrap support (500 pseudoreplicates) are indicated. Sequences in blue are up-regulated in both CUBA-DELTA and CAYMAN strains from the current study. Sequences underlined are over expressed in ≥2 populations versus laboratory susceptible strains from previously published studies (see text for further details). Sequences marked with * have proven ability to metabolise pyrethroids (Stevenson et al, submitted).</p

Detoxification genes differentially expressed in pyrethroid resistant populations relative to the susceptible NO strain.

<p>Detoxification genes differentially expressed in pyrethroid resistant populations relative to the susceptible NO strain.</p