Computational protocol: Grandpaternal-induced transgenerational dietary reprogramming of the unfolded protein response in skeletal muscle

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Protocol publication

[…] The transcriptomic data were analyzed using GSEA (Broad Institute; MA, USA, accessed at http://software.broadinstitute.org/gsea/). The data set was collapsed and the probe with the highest expression level for each respective gene was used for the enrichment analysis. Gene set permutation was used and a nominal p-value <0.05, and FDR <0.05 were considered significant , . Heatmaps were created using the online source Morpheus (Broad Institute; MA, USA, accessed at https://software.broadinstitute.org/morpheus/). PCA was performed for both transcriptomic and lipidomic data using the SIMCA 14.0 software (Umetrics, Umeå, Sweden). Log2 transformed data was used for further interaction analysis of the transcriptomic and lipidomic results applying the O2PLS method , using the SIMCA 14.0. […]

Pipeline specifications

Software tools GSEA, OmicsPLS
Application Protein interaction analysis
Organisms Homo sapiens, Rattus norvegicus
Chemicals Glucose