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Protein functions were predicted using the GO terms and manually curated using the information from the UniProt database, the National Center for Biotechnology Information (NCBI), and the literature data46.
Data and associated metadata were manually curated using the following inclusion criteria: i) experiments that did not induce genetic mutations, ii) experiments performed on Caco-2 cell monolayers that were grown for at least seven days and iii) arrays probing for at least 17000 genes (annotated in Chip Definition Files), thereby leaving out old arrays.
The data was manually curated using a structured-wiki platform.
These selected SNPs were manually curated using Integrative Genomics Viewer (IGV, Broad Institute) software.
Following the automatic positioning of enzyme nodes, several nodes were manually curated using Adobe Illustrator CS3 13.0.2 for layout optimization.
Select loci were manually curated using previously published N. meningitidis and N. gonorrhoeae genome sequences as references.
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Results were manually validated and curated using BLASTP analysis using transportDB [ 109] and taking into account orthology relationships.
The automated annotation results were then manually inspected and curated using Manatee (http://manatee.sourceforge.net, last accessed November 19 , 2013.
Full-length MSAs including the protein domain annotation were visualized and manually inspected and curated using the Jalview [ 69] alignment editor.
The gene-reaction associations were further manually verified and curated using the Enzyme Commission (EC) numbers from the functional annotation to correct for erroneous gene-reaction associations.
The putative microRNAs identified by miRDeep were further manually annotated and curated using both the UCSC genome browser (hg38) and miRBase (v.21).
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