Computational protocol: Metabolomic mechanisms of gypenoside against liver fibrosis in rats: An integrative analysis of proteomics and metabolomics data

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Protocol publication

[…] Protein identification and quantification were performed with Maxquant Proteins were considered up- or down-regulated if the fold change ≥ 1.2 or ≤ 0.83, respectively. Heatmap was carried out using SBC analysis system (SBC Shanghai Biotechnology Co., Ltd., Shanghai, China). Log-log plot was generated by GraphPad Prism 5.0 (San Diego, California, USA). Gene ontology (GO) and pathway analysis was performed using DAVID database ( identification and quantification were carried out using Agilent MSD workstation. Data was normalized with the sum of all peaks, and then normalized data was imported to SIMCA-P 11 (Umetrics AB, Umea, Sweden) for principle component analysis (PCA), partial least squares-discriminant analysis (PLS-DA) and orthogonal partial least squares (OPLS). The permutation analysis was performed by the PLS-DA. The calculation of variable importance in the projection (VIP) was got by the OPLS. Metabolites were considered statistically significant if VIP > 1 and P value <0.05. Identification was performed by searching in NIST database, and pathway analysis was carried out in KEGG database ( data of pharmacological evaluation were expressed as mean ± SD and statistically analyzed using One-Way ANOVA test (SPSS 16.0, Chicago, IL, USA), and P value <0.05 was considered statistically significant. […]

Pipeline specifications

Software tools MaxQuant, DAVID
Application MS-based untargeted proteomics
Diseases Liver Cirrhosis
Chemicals Aldehydes, Carbon Tetrachloride, Fructose, Glutathione, Glycine, Mannose, Sulfur