# Dietary Soy Impact on Host Transcriptome Profile--A Review
## 2 Materials and Methods  
In order to retrieve the current data on transcriptomic changes upon whole soybean (+/- soy protein) diet supplementation, we searched PubMed [43] using the keywords \"soy diet\", \"transcriptome\", \"nutrigenomics\", and gene expression regulation\". Exclusion criteria were as follows: experiments using only soy components (proteins, genistein, saponins, etc.) instead of whole soybean/soybean + soy proteins, lack of high throughput methods (microarray or next-generation sequencing), and written in a language other than English. At the end of the selection process, only eight studies were included in the analysis. The details regarding the animal species used, the characteristics of the dietary intervention (composition, duration), tissues analyzed, and the analytical platform used are presented in Table 1.  
We retrieved the sets of differentially expressed genes (as communicated by the authors) and subjected them to gene ontology/KEGG pathway overrepresentation analysis using the STRING platform, version 11.0 ([[http://string-db.org/](http://string-db.org/)]([http://string-db.org/](http://string-db.org/))), accessed on 21 May 2021). (using FDR = 0.05 as cutoff). The flowchart of our research work is presented in Figure 1. This represents Method 1.  
To identify which soy-induced pathways changes are conserved in evolution, we aggregated the transcriptome data based on their phyla source: fish (Atlantic salmon, zebrafish, yellow perch) and mammals (rats, mice, humans). After removing the duplicates, we performed a novel STRING analysis (FDR < 0.05) of differentially expressed genes and compared the significant KEGG pathways from the fish group with those in the mammal group. This represents Method 2.  
\begin{table}
\begin{tabular}{c c c c c} \hline \hline
**Species** & **Soy Diet** & **Duration of Feeding** & **Tissue** & **Analytical Platform** & **Ref.** \\ \hline Male rats (_Rattus norvegicus_) & Regular chow diet containing 20\% soybean meal & 18 months & Anterior pituitary and hypothalamus & Microarray & [44] \\ \hline Male rats (_Rattus norvegicus_) & Regular chow containing 20\% soybean + 7\% soybean oil & 7 days & Liver & RNA-seq & [45] \\ \hline Male mice (_Mus musculus_) & Regular chow containing 25\% soybean meal & 28 days & Liver & RNA-seq/Microarray & [46] \\ \hline Human (_Homo sapiens_) & Different soy foods & 12 months & Tumor Tissue & NanoString nCounter & [47] \\ breast cancer patients & & & & \\ \hline Atlantic salmon (_Salmo salar_) & Regular chow containing 20\% soybean meal + 10\% soybean meal + 2\% soybean & 36 days & Distal intestine & RNA-seq & [48] \\ \hline Atlantic salmon (_Salmo salar_) & Regular chow containing 45\% soy protein/Regular chow containing 36\% soybean meal & 8 weeks & Distal intestine & Microarray & [49] \\ \hline Yellow perch (_Perca favescens_) & Regular chow containing 75\% soybean meal & 61 days & Mid intestine & RNA-seq & [50] \\ \hline Zebrafish (_Danio rerio_) & Regular chow containing 50\% soybean meal + 2\% soybean saponin & 53 days & Intestine & RNA-seq & [51] \\ \hline \hline \end{tabular}
\end{table}
Table 1: Experimental conditions of studies reporting transcriptomic changes upon soy ingestion.