To identify a gene expression signature that faithfully reflects HIR in human liver, i.e., a HIR signature, we acquired gene expression data from liver biopsies of liver transplantation and hepatectomy patients from the National Center for Biotechnology Information's Gene Expression Omnibus database. The first and second sets of biopsies were taken from the livers of deceased donors (n = 13) and living donors (n = 8), respectively (GSE12720) [26] (link). The first core biopsies were taken before manipulation of the liver, and the second biopsies were taken after reperfusion following completion of bile duct anastomosis. A third set of biopsies was taken before and after surgery from remnant liver of patients who had undergone partial hepatectomy as treatment for colon cancer metastasis or hepatoblastoma (n = 4, GSE15239).
Gene expression data from cohort 1 were generated using the Illumina microarray platform HumanHT-12 version 4. Briefly, total RNA was extracted from fresh-frozen tissues using a mirVana RNA isolation and labeling kit (Ambion). For each sample, 500 ng of total RNA was used for labeling and hybridization according to the manufacturer's protocols. After the bead chips were scanned with an Illumina BeadArray Reader, the microarray data were normalized using the quantile normalization method in the Linear Models for Microarray Data package in the R language environment [27] (link). The expression level of each gene was transformed into log2 base before further analysis. Primary microarray data from human liver tissues are available in the National Center for Biotechnology Information's Gene Expression Omnibus public database (accession number GSE39791).
Gene expression data from cohort 1 were generated using the Illumina microarray platform HumanHT-12 version 4. Briefly, total RNA was extracted from fresh-frozen tissues using a mirVana RNA isolation and labeling kit (Ambion). For each sample, 500 ng of total RNA was used for labeling and hybridization according to the manufacturer's protocols. After the bead chips were scanned with an Illumina BeadArray Reader, the microarray data were normalized using the quantile normalization method in the Linear Models for Microarray Data package in the R language environment [27] (link). The expression level of each gene was transformed into log2 base before further analysis. Primary microarray data from human liver tissues are available in the National Center for Biotechnology Information's Gene Expression Omnibus public database (accession number GSE39791).
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