Differentiating between liver diseases by applying multiclass machine learning approaches to transcriptomics of liver tissue or blood-based samples

Asrani, 2019, Burden of liver diseases in the world, J Hepatol, 70, 151, 10.1016/j.jhep.2018.09.014 Shasthry, 2016, New treatment options for alcoholic hepatitis, World J Gastroenterol, 22, 3892, 10.3748/wjg.v22.i15.3892 Torruellas, 2014, Diagnosis of alcoholic liver disease, World J Gastroenterol, 20, 11684, 10.3748/wjg.v20.i33.11684 Singh, 2019, Assessing liver fibrosis without biopsy in patients with HCV or NAFLD, Cleve Clin J Med, 86, 179, 10.3949/ccjm.86a.17118 Ibn Sina, 2018, Epigenetically reprogrammed methylation landscape drives the DNA self-assembly and serves as a universal cancer biomarker, Nat Commun, 9 Berdasco, 2019, Clinical epigenetics: seizing opportunities for translation, Nat Rev Genet, 20, 109, 10.1038/s41576-018-0074-2 Nallagangula, 2018, Liver fibrosis: a compilation on the biomarkers status and their significance during disease progression, Future Sci Oa, 4, 10.4155/fsoa-2017-0083 Ding, 2015, Characterisation of peripheral blood mononuclear cell microRNA in hepatitis B-related acute-on-chronic liver failure, Sci Rep, 5, 10.1038/srep13098 Waldron, 2015, Peripheral blood mononuclear cell gene expression remains broadly altered years after successful interferon-based hepatitis C virus treatment, J Immunol Res, 2015 Zhang, 2014, Gene expression profiles of peripheral blood mononuclear cells in primary biliary cirrhosis, Clin Exp Med, 14, 409, 10.1007/s10238-013-0253-6 Zhou, 2016, Comparative transcriptome analysis of peripheral blood mononuclear cells in hepatitis B-related acute-on-chronic liver failure, Sci Rep, 6 Sowa, 2014, Non-invasive separation of alcoholic and non-alcoholic liver disease with predictive modeling, PLos One, 9, 10.1371/journal.pone.0101444 Trepo, 2018, Combination of gene expression signature and model for end-stage liver disease score predicts survival of patients with severe alcoholic hepatitis, Gastroenterology, 154, 965, 10.1053/j.gastro.2017.10.048 Hoshida, 2013, Prognostic gene expression signature for patients with hepatitis C-related early-stage cirrhosis, Gastroenterology, 144, 1024, 10.1053/j.gastro.2013.01.021 Sheng, 2017, Multi-perspective quality control of Illumina RNA sequencing data analysis, Brief Funct Genomics, 16, 194 Dobin, 2013, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 15, 10.1093/bioinformatics/bts635 Massey, 2021, Integrated multiomics reveals glucose use reprogramming and identifies a novel hexokinase in alcoholic hepatitis, Gastroenterology, 160, 1725, 10.1053/j.gastro.2020.12.008 Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, 15, 10.1186/s13059-014-0550-8 Trapnell, 2012, Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nat Protoc, 7, 562, 10.1038/nprot.2012.016 Saeys, 2007, A review of feature selection techniques in bioinformatics, Bioinformatics, 23, 2507, 10.1093/bioinformatics/btm344 Pedregosa, 2011, Scikit-learn: machine learning in Python, J Machine Learn Res, 12, 2825 Chen, 2013, Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool, BMC Bioinform, 14, 10.1186/1471-2105-14-128 Krämer, 2014, Causal analysis approaches in ingenuity pathway analysis, Bioinformatics, 30, 523, 10.1093/bioinformatics/btt703 Mootha, 2003, PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes, Nat Genet, 34, 267, 10.1038/ng1180 Rinchai, 2021, BloodGen3Module: blood transcriptional module repertoire analysis and visualization using R, Bioinformatics, 37, 2382, 10.1093/bioinformatics/btab121 Sharma, 2021, Differential blood transcriptome modules predict response to corticosteroid therapy in alcoholic hepatitis, JHEP Rep, 3 Anderson, 2013, Iron homeostasis in the liver, Compr Physiol, 3, 315, 10.1002/cphy.c120016 Gkamprela, 2017, Iron deficiency anemia in chronic liver disease: etiopathogenesis, diagnosis and treatment, Ann Gastroenterol, 30, 405 Hong, 2019, Erythropoietin suppresses hepatic steatosis and obesity by inhibiting endoplasmic reticulum stress and upregulating fibroblast growth factor 21, Int J Mol Med, 44, 469 Sun, 2020, Function of TREM1 and TREM2 in liver-related diseases, Cells, 9, 2626, 10.3390/cells9122626 Zimmermann, 2011, Interleukin-8 is activated in patients with chronic liver diseases and associated with hepatic macrophage accumulation in human liver fibrosis, PLoS One, 6, 10.1371/journal.pone.0021381 Tan, 2013, IL-17A plays a critical role in the pathogenesis of liver fibrosis through hepatic stellate cell activation, J Immunol, 191, 1835, 10.4049/jimmunol.1203013 Chai, 2017, Estrogen-metabolizing enzymes in systemic and local liver injuries: a case study of disease-drug interaction, Drug Metab Dis, 241, 10.1016/B978-0-12-802949-7.00010-9 Pettinelli, 2018, Altered hepatic genes related to retinol metabolism and plasma retinol in patients with non-alcoholic fatty liver disease, Plos One, 13, 10.1371/journal.pone.0205747 Saeed, 2018, Disturbed vitamin A metabolism in non-alcoholic fatty liver disease (NAFLD), Nutrients, 10 Kanno, 2019, Serum aldo-keto reductase family 1 member B10 predicts advanced liver fibrosis and fatal complications of nonalcoholic steatohepatitis, J Gastroenterol, 54, 549, 10.1007/s00535-019-01551-3 Ye, 2019, A large-scale multicenter study validates aldo-keto reductase family 1 member B10 as a prevalent serum marker for detection of hepatocellular carcinoma, Hepatology, 69, 2489, 10.1002/hep.30519 Sayaf, 2022, The nuclear receptor PXR in chronic liver disease, Cells, 11, 61, 10.3390/cells11010061 Teschke, 2018, Alcoholic liver disease: alcohol metabolism, cascade of molecular mechanisms, cellular targets, and clinical aspects, Biomedicines, 6, 10.3390/biomedicines6040106 Wang, 2019, CYP2A6 is associated with obesity: studies in human samples and a high fat diet mouse model, Int J Obes, 43, 475, 10.1038/s41366-018-0037-x Naim, 2017, Matrix metalloproteinases (MMPs) in liver diseases, J Clin Exp Hepatol, 7, 367, 10.1016/j.jceh.2017.09.004 Su, 2017, Requirement of cytosolic phospholipase A2 gamma in lipid droplet formation, Biochim Biophys Acta Mol Cell Biol Lipids, 1862, 692, 10.1016/j.bbalip.2017.03.007 Narayana, 2015, The interferon-induced transmembrane proteins, IFITM1, IFITM2, and IFITM3 inhibit hepatitis C virus entry, J Biol Chem, 190, 25946, 10.1074/jbc.M115.657346 Vafaee, 2018, A data-driven, knowledge-based approach to biomarker discovery: application to circulating microRNA markers of colorectal cancer prognosis, NPJ Syst Biol Appl, 4, 10.1038/s41540-018-0056-1