Computational protocol: iTRAQ-Based Proteomics Identification of Serum Biomarkers of Two Chronic Hepatitis B Subtypes Diagnosed by Traditional Chinese Medicine

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Protocol publication

[…] To identify differentially expressed proteins in LSSD-CHB and DHSM-CHB compared to HCTL, we set a cut-off for fold change (>1.2) of protein abundance provided by Mascot and p value (<0.05) calculated by edgeR []. Venn diagram of up- and downregulated proteins was analyzed by InteractiVenn (http://www.interactivenn.net/) []. To annotate potential functions of proteins, UniProt IDs of candidate proteins were submitted to DAVID Bioinformatics Resources 6.7 (https://david.ncifcrf.gov/home.jsp) [] and STRING v10 (http://string-db.org/) [], Gene Ontology (GO), and KEGG pathway were selected, and we used false discovery rate (FDR) to control the results. Protein-protein interaction networks were analyzed by STRING. […]

Pipeline specifications

Software tools edgeR, InteractiVenn, DAVID
Databases KEGG PATHWAY
Application Protein interaction analysis
Organisms Homo sapiens
Diseases Hepatitis B, Carcinoma, Hepatocellular, Infection, Splenic Neoplasms, Hepatitis B, Chronic