Confirmation of Affymetrix microarray data by RT-PCR.

<p><i>GAPDH</i>, a housekeeping gene, was used to normalize gene expression in human and mouse (a) PFC, (b) HIP and (c) STR. Genes that are predicted by miacroarray data but not verified by RT-PCR are highlighted using dashed boxes. The background and band colors were reversed. The average relative densitometry values were analyzed using Image J software. Data are expressed as mean ± SD. Red bars represent human and green bars mouse.</p

Confirmation of Affymetrix chip data by qRT-PCR.

<p>GAPDH was used to normalize gene expression. The relative expression of each gene was calculated as log2 of 2^-△Ct values. Data are expressed as mean ± SD. Red bars represent human and green bars mouse.</p

Neurobiological roles of species-specific expressed orthologous genes.

<p>Neurobiological roles of species-specific expressed orthologous genes.</p

The number of the notably enriched BP terms of the highly expressed genes.

<p>The number of the significantly enriched BP terms (a) and neuro-related BP terms (b). DAVID was selected to perform functional enrichment analysis. The statistical significance is determined using the one-tailed Fisher’s exact test followed by the Benjamini correction; adjusted p < 0.01 was considered significant. Red bars represent human and blue bars mouse.</p

Gene expression pattern analysis.

<p>(a) Hierarchical clustering dendrogram of the 12 datasets (distance metric: “1-P”, linkage method: complete). The color bars below the dendrogram provide information about the species (upper bar) and the datasets (lower bar). (b) Principal component analysis (PCA) of the 12 datasets. Brain tissues are labeled by different colors (green = PFC; red = HIP; blue = STR). Microarray platforms are labeled by different shapes (circle = HG-U133_Plus_2; triangle = HG-U133A; square = Mouse430_2; hexagon = Mouse430A_2). The ellipse shows 95% confidence intervals.</p

Overlapping ratio and semantic similarity analyses.

<p>(a) Comparison of the overlapping ratios. The overlapping ratio was defined as the number of the intersection divided by the number of the union of two BP term sets. The overlap significance was determined using the one-tailed Fisher’s exact test. Hierarchical clustering with a Pearson distance metric and average linkage method was performed based on the overlapping ratios. (b) Comparison of the semantic similarities. Semantic similarity between two sets of BP terms was measured using mgoSim function from an R package termed GOSemSim. The method parameter was set as “Wang” and the GO used in measurement was restricted by assigning the corresponding parameter to ‘BP’. The similarity score is between 0 and 1. The higher the score, the more similarity between two sets of BP terms. Hierarchical clustering with a Pearson distance metric and average linkage method was performed based on the calculated similarity scores.</p