2.1. In silico networking of SE‐host genomics: initial material for interpretation

Systematic reviews are a valuable tool for acquiring concepts, identifying gaps in knowledge and prioritizing areas for future research in chicken genomics research on SE. For this reason, the Preferred Reporting Items for Systematic reviews and Meta‐Analyses protocol was used to conduct a systematic review of significant candidate genes affecting SE (Woods et al., 2006). A total of 40 journal articles were collected and studied for the primary study, and those with low validity were not included in the subsequent analysis. Search engines, Science Direct, PubMed, SCIRUS, Google Scholar, Oxford Journals, Cambridge Journals, Springer Journals, Wiley Library and the NCBI website were the sources of new material for this report. Salmonella, candidate gene, quantitative trait locus (QTL) mapping, gene expression, connectivity and gene ontology, genome‐wide association studies and RNA‐Seq profiles were the most frequently selected keywords to search for the target papers.

The majority of the papers were written in English, and the search was strictly limited to the Gallus gallus species. Paper sorting and deduplication were done using Endnote software. In summary, results from text‐based surveys and online computational tools from Phenomenon (https://genemania.org) have been translated to a significant statistical level for Salmonella‐associated genomic regions and their network pathways using in silico models in sheep, and the reader is provided with a short list of the most important genes involved in SE. Criteria for connectivity assessed were inter‐centrality, properties, co‐expression, expected genetic interactions, signalling pathways, physical interactions, shared protein domains and co‐locations. Table 1 indicates a snapshot of the gene list associated with the immune system in G. gallus species genome.

Snapshot of gene list associated with immune system in Gallus gallus species genome.