Gene

[…] , DIP [] and IntAct [] and filtered them to retain the interactions from cow, human, mouse, pig, rabbit and rat. The gene or protein identifiers were then converted to Ensemble gene identifiers using Entrez [] gene-to-Ensembl mapping for BioGRID or UniProt-SwissProt []-to-Ensembl mapping for MINT, DIP and IntAct. The mapping of gene homology between each of the selected species and cow was obtaine […]

[…] . KEGG database was used to classify the genes with significant differential expression based on their functions. The online software DAVID Bioinformatics Resources 6.8 was used to convert gene ID to ENTREZ_GENE_ID (https://david.ncifcrf.gov/content.jsp?file=functional_classification.html). The Pathway Enrichment Analysis tool Omicshare was used to classify genes at the level of KEGG_B_class (http […]

[…] r multiple tests (). Genes were considered significantly differentially expressed (DE) using an FDR-adjusted P value of <0.01 and an estimated log2 fold change (log2FC) beyond ±1, giving 1,526 unique Entrez Gene identifiers considered to be DE. The set of DE identifiers was tested for enrichment of Gene Ontology (GO) terms using the Fisher exact test and a set of background genes, defined as those […]

[…] udies have also carried out normalisation whilst making no distinction between genes/proteins. For example, Dogan et al. [] annotated genes/proteins of interest and manually added their corresponding Entrez Gene identifiers. There are, however, studies that have a list of multiple types of biomedical entities, such as PubTator [], and BEST []. PubTator considers 5 biomedical entities and BEST cons […]

[…] ext, pathways enriched by the targets of each compound were identified. For this purpose, 2010 human pathways and their associated genes from the Biosystems [] database were extracted. The equivalent Entrez gene IDs of each protein target of compounds were retrieved using Biomart []. For each compound a list of, on average, six gene IDs that the compound is predicted to interact with (the ‘compoun […]

[…] s used to rank the genes.Genes from significant modules identified in the WGCNA analysis were used for functional enrichment analysis using ClueGO v.2.5.0 with a Cytoscape v3.4.0 plugin []. The ovine Entrez gene IDs from each module was used as input and all ovine Entrez gene IDs included in the co-expression analysis was used as Custom Reference Set.Significance threshold for KEGG pathway and GO […]