Computational protocol: Regressive Effect of Myricetin on Hepatic Steatosis in Mice Fed a High-Fat Diet

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Protocol publication

[…] In order to find the possible mechanism for ameliorative effects of myricetin on HFD-induced hepatic steatosis, microarray analysis was used to have a wide understanding of the altered genes and pathways that might be involved. Nimblegen gene chip microarray analysis was performed at CapitalBio Corporation (Beijing, China). Samples from HFD and HM groups were isolated from the frozen livers (n = 3 for each group) using Trizol reagent (Invitrogen, Carlsbad, CA, USA) and was further purified using NucleoSpin® RNA clean-up (Macherey-Nagel, Duren, Germany). Array hybridization, washing, and scanning were conducted according to the Nimblegen’s Expression user’s guide. In a comparison analysis, two-class unpaired method in the Significant Analysis of Microarrays (SAM, version 3.02, Stanford University, Stanford, CA, USA) was performed to identify significantly differentially expressed genes (DEGs) between HFD and HM groups. The DEGs were selected and put into Pathway-Express in Onto-Tools []. Pathway-Express searches the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database for each input gene, and the impact analysis was performed in order to build a list of all associated pathways []. An impact factor (IF) is calculated for each pathway incorporating parameters, such as the normalized fold change of the DEGs, the statistical significance of the set of the pathway genes, and the topology of the signaling pathway. The corrected gamma p-value is the p-value provided by the impact analysis. The differences were considered to be significant when the corrected gamma p-value was less than 0.05. […]

Pipeline specifications

Software tools Pathway-Express, Onto-Tools
Application ChIP-on-chip analysis
Organisms Mus musculus
Diseases Fatty Liver, Liver Diseases, Metabolic Diseases
Chemicals Glutathione, Heme, Superoxides