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Each category (i.e. F, U, D) defined the result of the analysis between two adjacent developmental times.
This conservative strategy selected probe sets that were differentially expressed between two adjacent developmental times with the highest level of confidence.
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Each symbol (D, U, F) represents the direction of change in gene expression between any two adjacent developmental time points.
The gene expression data were subjected to statistical analysis to identify genes that were significantly differentially expressed between any two adjacent developmental time points.
Each dataset was independently analyzed by employing the statistical procedures described below to identify probe sets that were significantly differentially expressed between any two adjacent developmental times.
Genes that were significantly differentially expressed between any two adjacent developmental time points, as measured by the convergence of the three analysis methods, are listed in Additional File 1.
Although S2 and S3 stages were developmentally adjacent to each other with only 9 hours of interval, they were clustered in two separate groups, which is consistent to the dramatic increase in mRNA complexity and the highest number of differentially regulated genes observed between the two adjacent developmental stages.
Some modules might correlate with two adjacent developmental stages because of the similarity of these two adjacent developmental stages.
Comparison of any two adjacent developmental stages shows that 3267 genes changed significantly in their mRNA accumulation.
When the number of developmental stages within a day is not an integer, the larval cohort is distributed into two adjacent developmental stages in proportions that preserve the average development rate.
As the developmental changes between two adjacent stages vary during embryogenesis and may thus involve genes whose expression is only altered between these two adjacent stages, we examined the number of genes that were regulated only between any adjacent two stages, which we termed "uniquely regulated genes" (Additional file 2).
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