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Gene signature-based classification of samples The MetaIntegrator R package 99 was used for evaluating gene biomarkers in the present RNA-seq dataset and public microarray and RNA-seq datasets

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The centroided data were searched using a custom Python script Mighty_skeleton v.0.0.2 and peak heights were extracted from the mzXML files based on a previously established library of metabolite retention times and accurate masses adapted from the Whitehead Institute 69 and verified with authentic standards and/or high resolution MS/MS spectral manually curated against the NIST14MS/MS 70 and METLIN (2017) 71 tandem mass spectral libraries