Using the Ensembl mouse gene dataset [ 14] as reference, we identified 9,395 protein-coding genes with one-to-one orthology between diverse mammalian taxa, including whales, a bat, rodents, a tree shrew and a primate (Fig. 2A).
Mouse gene expression datasets generated by Mouse Genome 430 2.0 Array (Affymetrix) and raw data files (.cel) were obtained from the GEO database for developing heart valves (E12.5 ECCs and E17.5 valves [GSE11040]), and developing forelimb buds (E10.5 forelimb buds and E13.5 forelimb buds [GSE30138]) [ 10, 20].
The 14th dataset GSE2514 in Table 1 that is a mouse gene expression dataset was not applied to the diagram in Figure 1 and was not included in calculating the accuracy of prediction in the meta-analysis.
The entire mouse gene expression dataset was standardized employing principal components of the Affymetrix control probe sets [ 24].
The mouse gene expression dataset was based on Q-PCR experiments, performed by Bookout et al., [ 2], for all 49 mouse NR genes, over 39 normal tissues, repeated in two mouse strains (C57Bl/6J & 129x1/SvJ).
When our mouse gene expression dataset was compared to an additional profiled cohort of human alcoholics [ 15], we consistently found a highly significant match among differentially expressed genes between the mouse and human models (84 common differentially expressed genes, P < 1 × 10-7, (Additional file 1: Figure S1B).
These maps have been constructed from the expression levels of 19,727 human genes in 4164 datasets and 22,766 mouse genes in 3571 datasets from the GEO database [ 27].
We created four groups of datasets (each group includes 20 human and 20 mouse gene expression matrixes) by randomly removing 5 %, 10 %, 15and 20% and 20%f the origenes datasets, we then identified the mofules using the aboriginalionedatasetsch.
However, the rapidly accumulating datasets will help complete a mouse gene annotation.
The D. melanogaster dataset was obtained by combining gene expression datasets from [ 17] and [ 30]; mouse gene expression data were obtained from [ 6].
