Finally we obtained 14036 and 13134 human and mouse gene datasets with AP annotations, respectively.
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).
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].
To assess phylogenetic affinities among the presently-documented Streptococcus species and the bacterium identified in Marion Island mouse kidneys, a 16S gene dataset was compiled comprising 37 Streptococcus type specimen sequences, the Mus kidney Streptococcus sequence generated in this study, and four Enterococcus sister-taxon sequences.
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].
In addition, mouse 3'UTRs of the known gene dataset were downloaded from table browser at: http://genome.cse.ucsc.edu/cgi-bin/hgTables and were analyzed for repeats utilizing the local RepeatMasker.
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.
