An expression map for Anopheles gambiae

Abstract

Background: Quantitative transcriptome data for the malaria-transmitting mosquito Anopheles gambiae covers a broad range of biological and experimental conditions, including development, blood feeding and infection. Web-based summaries of differential expression for individual genes with respect to these conditions are a useful tool for the biologist, but they lack the context that a visualisation of all genes with respect to all conditions would give. For most organisms, including A. gambiae, such a systems-level view of gene expression is not yet available.

Results: We have clustered microarray-based gene-averaged expression values, available from VectorBase, for 10194 genes over 93 experimental conditions using a self-organizing map. Map regions corresponding to known biological events, such as egg production, are revealed. Many individual gene clusters (nodes) on the map are highly enriched in biological and molecular functions, such as protein synthesis, protein degradation and DNA replication. Gene families, such as odorant binding proteins, can be classified into distinct functional groups based on their expression and evolutionary history. Immunity-related genes are non-randomly distributed in several distinct regions on the map, and are generally distant from genes with house-keeping roles. Each immunity-rich region appears to represent a distinct biological context for pathogen recognition and clearance (e.g. the humoral and gut epithelial responses). Several immunity gene families, such as peptidoglycan recognition proteins (PGRPs) and defensins, appear to be specialised for these distinct roles, while three genes with physically interacting protein products (LRIM1/APL1C/TEP1) are found in close proximity.

Conclusions: The map provides the first genome-scale, multi-experiment overview of gene expression in A. gambiae and should also be useful at the gene-level for investigating potential interactions. A web interface is available through the VectorBase website http://www.vectorbase.org/. It is regularly updated as new experimental data becomes available.

Figure 1

The A. gambiae expression map. Expression data from all publicly available experiments, representing 93 assay conditions, was summarised for 10194 genes and clustered using the self-organizing map algorithm. The area of the grey circles represents the number of genes mapping to each discrete node on the map (minimum 1, maximum 114). The four panels show the same map with different annotations that indicate regions of the map associated with high expression in various conditions: a Development from embryo to adult male and female [8,10]; b Embryonic development [17]; c Organs and tissues [8,10,11,17]; d Uninfected blood meal time course [8] (BF: blood fed, NBF: non-blood fed).

Figure 2

Regions of the map are enriched with different gene functions. Genes annotated with a selection of (highly enriched on a per-node basis) Gene Ontology terms are indicated by the coloured pie charts in each node. The corresponding regions marked with coloured lines are described according to their gene expression characteristics. The Gene Ontology terms are as follows: orange, GO:0003735, structural constituent of ribosome; light blue, GO:0051082, unfolded protein binding; green, GO:0000502, proteasome complex; yellow, GO:0006260, DNA replication; dark blue, GO:0031497, chromatin assembly; vermillion, GO:0015078, hydrogen ion transmembrane transporter activity; purple, GO:0005549, odorant binding; black, GO:0042302, structural constituent of cuticle.

Figure 3

Multi-experiment maps cluster genes by function to a greater extent than single experiment maps. The number of enriched non-redundant Gene Ontology terms is shown for three significance thresholds for six different maps: three single experiment maps, two maps made with older versions of the VectorBase expression data, and the map using current data as shown in previous figures. The multi-experiment maps show substantially more clustering of genes by biological process and molecular function than the single experiment maps. Full details of the maps and datasets can be found in Table 4.

Figure 4

Odorant binding proteins (OBPs) are found in several distinct regions of the expression map, which generally correspond to paralogous groups. The OBP paralogous groups (OBP-PGs) are defined (top). OBPs are shown as coloured pie sections on the expression map (centre) with regions of interest are outlined and annotated in terms of two major expression characteristics. The pie charts of four map nodes dominated by OBPs are shown at greater magnification (bottom left and right).

Figure 5

Immunity genes are highly localised. Genes belonging to various immunity-related pathways and gene families are shown on the map. Toll pathway members are labeled in dark cyan, the IMD pathway in dark red, JAK/STAT pathway in yellow, siRNA pathway in bright green, anti-microbial peptides and effectors in magenta, and LRIM1, APL1C and TEPs are labeled in dark green. CLIP-domain serine proteases, serpins, C-type lectins and galectins are shown generically in black, light red, black italic and cyan respectively. Several regions of the map that are rich in immunity genes are outlined and described by their dominant gene expression characteristics.