Computational protocol: Gene expression profiling of peripheral blood mononuclear cells in the setting of peripheral arterial disease

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Protocol publication

[…] To assess the functional repertoire of differentially expressed genes we adopted a multi-tiered bioinformatics annotation pipeline with functional enrichment calculations, pathway and molecular event analysis, biological network analysis and biocuration. Statistically significant genes and annotations were used as pointers to perform literature curation to derive biological role of genes differentially regulated in the setting of PAD. Preliminary functional annotations of differentially regulated genes were derived using BioGPS [].GO term enrichment analysis was performed using DAVID v6.7 [,]. As no single annotation resource provides information about all available biological pathways, we used two different pathway databases (Reactome v36.2 [] and Kyoto Encyclopedia of Genes and Genomes (KEGG) []) to identify the biological pathways mediated by differentially expressed genes. Reactome based pathway enrichment analysis was performed using Reactome Pathway Analysis tool http://www.reactome.org/ReactomeGWT/entrypoint.html#PathwayAnalysisDataUploadPage. This two-fold approach was useful in finding several relevant pathways from two different pathway analyses. Ingenuity Pathway Analysis® suite (IPA v9.0 - 3211, http://www.ingenuity.com) was used to understand functional networks involved in the gene sets. IPA-Tox®, a data analysis routine within IPA that assess potential toxicity with various compounds using toxicogenomics data was also used to interpret the functional context of differentially regulated genes. Finally, to understand the functional context and biological significance of differentially expressed genes relevant to PAD, scientific literature was curated using Gene Related InFormation (GeneRIF http://www.ncbi.nlm.nih.gov/projects/GeneRIF) and 'related articles by PubMed' in the 'Entrez Gene' http://www.ncbi.nlm.nih.gov/gene page. […]

Pipeline specifications

Software tools DAVID, IPA
Databases Reactome BioGPS
Application Drug design
Organisms Homo sapiens
Diseases Blood Platelet Disorders, Vascular Diseases, Atherosclerosis, Peripheral Arterial Disease
Chemicals Zinc