Meta-analysis of genome-wide expression patterns associated with behavioral maturation in honey bees

Abstract

Background: The information from multiple microarray experiments can be integrated in an objective manner via meta-analysis. However, multiple meta-analysis approaches are available and their relative strengths have not been directly compared using experimental data in the context of different gene expression scenarios and studies with different degrees of relationship. This study investigates the complementary advantages of meta-analysis approaches to integrate information across studies, and further mine the transcriptome for genes that are associated with complex processes such as behavioral maturation in honey bees. Behavioral maturation and division of labor in honey bees are related to changes in the expression of hundreds of genes in the brain. The information from various microarray studies comparing the expression of genes at different maturation stages in honey bee brains was integrated using complementary meta-analysis approaches.

Results: Comparison of lists of genes with significant differential expression across studies failed to identify genes with consistent patterns of expression that were below the selected significance threshold, or identified genes with significant yet inconsistent patterns. The meta-analytical framework supported the identification of genes with consistent overall expression patterns and eliminated genes that exhibited contradictory expression patterns across studies. Sample-level meta-analysis of normalized gene-expression can detect more differentially expressed genes than the study-level meta-analysis of estimates for genes that were well described by similar model parameter estimates across studies and had small variation across studies. Furthermore, study-level meta-analysis was well suited for genes that exhibit consistent patterns across studies, genes that had substantial variation across studies, and genes that did not conform to the assumptions of the sample-level meta-analysis. Meta-analyses confirmed previously reported genes and helped identify genes (e.g. Tomosyn, Chitinase 5, Adar, Innexin 2, Transferrin 1, Sick, Oatp26F) and Gene Ontology categories (e.g. purine nucleotide binding) not previously associated with maturation in honey bees.

Conclusion: This study demonstrated that a combination of meta-analytical approaches best addresses the highly dimensional nature of genome-wide microarray studies. As expected, the integration of gene expression information from microarray studies using meta-analysis enhanced the characterization of the transcriptome of complex biological processes.

Figure 1

Venn diagram of the number of differentially expressed transcripts detected by at least two individual-study analyses (Ind), study-level (Study), and sample-level (Sample) meta-analyses.

Figure 2

Funnel plots of differential expression estimates and 95% confidence interval limits for Apis mellifera transcripts BB170018A20B07 (2A), BB170024B10C11 (2B), BB170024B20H07 (2C), and BB170004B20H08 (2D), by individual-study, study-level (Study), non-standardized study-level (N_Study), and sample-level (Sample) meta-analyses. Estimates and 95% confidence intervals for each analysis are represented by a square and a horizontal line, respectively. Study denotes study-level meta-analysis of standardized estimates, N_Study denotes study-level meta-analysis of non-standardized estimates, Sample denotes sample-level meta-analysis. AC: Apis cerana bees raised on Apis cerana colonies; AD: Apis dorsata bees raised on Apis dorsata colonies; AF: Apis florea bees raised on Apis florea colonies; AM: Apis mellifera bees raised on an Apis mellifera colony, LL: Apis mellifera ligustica bees raised on an Apis mellifera ligustica colony; LM: Apis mellifera ligustica bees raised on an Apis mellifera mellifera colony; ML: Apis mellifera mellifera bees raised on an Apis mellifera ligustica colony; MM: Apis mellifera mellifera bees raised on an Apis mellifera mellifera colony The size of the square denoting the estimate corresponds to the number of observations in the study (AC, AD, AF n = 24; AM n = 22; LL, LM, ML, MM n = 12; study-level (Study) meta-analysis n = 8; sample-level (Sample) meta-analysis n = 142). Analyses detecting significant (P-value < 1 × 10^-3) differential expression between forager and one-day-old honey bees are denoted by an asterisk.