# Dietary Soy Impact on Host Transcriptome Profile--A Review
## 3 Results  
To our surprise, only eight reports matched our selection criteria and could be roughly divided into fish (four studies) and mammals (four studies). After removing the duplicates and the low confidence transcripts, the expression of 1.779 genes were reported as significantly altered in mammals, of which 838 (47.1%) were downregulated and 941 were upregulated. In the fish group, the expression of 1.524 genes was reported as significantly changed, of which 932 (61.1%) were downregulated and 592 were upregulated. The ratios between upregulated and downregulated genes in the two phyla are significantly different (\(p\)-value for the Z test \(<\) 0.00001). After combining fish and mammal data, 1770 (53.6%) genes were downregulated, and 1533 were upregulated upon soy diet intervention. All the upregulated and downregulated genes for both phyla groups and the commonly altered ones are shown in Supplementary Table S1. To better understand the biological significance of these changes, we decided to use two methods of analysis. We submitted each set of reported data to STRING analysis (using a medium confidence interaction score of 0.400), focusing on retrieving the enriched KEGG pathways (FDR \(<\) 0.05). We have chosen STRING, since it builds gene interaction networks based on experimental and co-expression data, thus reducing the noise inherent to expression data from multiple cell/tissue types. The gene networks obtained are of relatively low complexity, with statistically significant protein-protein interaction (PPI) enrichment obtained for only six datasets. Overall, 67 KEGG pathways in mammals and 72 KEGG pathways in fish are potentially altered by soy enriched diet, of which 22 are common to both phyla (Table 2). These common pathways might represent a response to the soy diet conserved between fish and mammals and include metabolic pathways, biosynthesis of unsaturated fatty acids, steroid biosynthesis, fatty acid metabolism, fatty acid elongation, retinol, and xenobiotic metabolism. These pathways include most of the candidate genes for diabetes, atherosclerosis, regulation of lipid metabolism. Of note, the shared, potentially conserved pathways  
Figure 1: Flowchart displaying the process of our systematic review study. are composed of different sets of altered genes, suggesting that distinct transcriptome changes mediate these common metabolic effects. Given that due to their size not all datasets allowed a successful STRING analysis, we performed a STRING/ KEGG pathway enrichment analysis on pooled transcriptome data from fish, respectively, mammal samples. The gene interaction networks were of higher complexity, with significantly higher PPI probabilities, thus richer information. Nevertheless, the KEGG pathway analysis results were similar: 61 KEGG pathways in fish, 55 pathways in mammals, of which 23 are common to both phyla (Table 3). The two analysis methods (Method 1 and Method 2) lead to 16 KEGG pathways that are common between fish and mammals (Figure 2). See Supplementary Table S2 for all the DEGs corresponding to each Common KEGG pathways of individual and pooled datasets (Method 1 and Method 2).