Computational protocol: Identification of key genes and pathways associated with classical Hodgkin lymphoma by bioinformatics analysis

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Protocol publication

[…] Several R packages was used for raw microarray data preprocessing, including concluding quality assessment (QA), quality control (QC), background correction and normalization. The R packages using for QA/QC were simpleaffy (), affyPLM and arrayQualityMetrics (). Through QC checks, the sample GSM312887 within the dataset was disqualified () and excluded from subsequent analysis. Robust multi-array average (RMA) () was used to perform background correction, normalization and probe summarization. The empirical Bayesian method in limma package () was used to perform the differential analysis, |log2 fold change (FC)| >2.5 and adjusted P<0.001 were considered as statistically significant. [...] The Search Tool for the Retrieval of Interacting Genes (STRING 10.0) is a database that was designed to predict the PPI between DEGs () and combination score >0.4 was considered to be significant. Cytoscape software was used to visualize the results of the PPI network (), the sub-networks of co-expression were constructed by ClusterONE () at the base of PPI network. ClusterONE is the plug-in component of Cytoscape designed to identify closely connected and potentially overlapping regions in the PPI network (ClusterONE parameters: Minimum size, 3; minimum density, 0; overlap threshold, 0.8). GO and KEGG pathway enrichment analysis of modular genes was implemented using the DAVID online tool. […]

Pipeline specifications

Software tools ClusterONE, DAVID
Databases KEGG PATHWAY
Application Protein interaction analysis
Diseases Hodgkin Disease, Neoplasms, Epstein-Barr Virus Infections
Chemicals Tyrosine