Computational protocol: Classical NF-κB Metabolically Reprograms Sarcoma Cells Through Regulation of Hexokinase 2

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Protocol publication

[…] Total RNA was isolated using a standard Trizol extraction protocol and purified with a cleanup kit (Qiagen). Affymetrix GeneChip Human Transcriptome Array 2.0 (Affymetrix) arrays were used for microarray. Probe intensity (CEL) files were obtained, and Affymetrix Transcriptome Analysis Console software was used for array analysis. Differentially expressed genes were identified by the Robust Multichip Average method ().Gene set enrichment analysis v2.0 was used to determine the enrichment of functional categories in the entire linear gene expression dataset (). GSEA was performed using MSigDB C2 CP: Canonical pathways gene set collection. Statistical significance was determined using 1,000 random permutations of each gene set to obtain a nominal p-value and false discovery rate. Heat map was generated using GenePattern (). HeatmapViewer (v11) was used to display values in heat map format for the genes identified from GSEA analysis.The microarray data have been deposited into the GEO database with the accession number GSE112119. […]

Pipeline specifications

Software tools TAC Software, GSEA, GenePattern, HeatMapViewer
Databases MSigDB
Applications Gene expression microarray analysis, Transcriptome data visualization
Diseases Neoplasms, Rhabdomyosarcoma, Sarcoma, Osteosarcoma