《Table 1The collected gene expression datasets in HCCDB》

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《HCCDB: A Database of Hepatocellular Carcinoma Expression Atlas》

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In the current database release，we archived 15 public HCC gene expression datasets containing totally 3917 samples（Table 1）.For 13 microarray datasets，probe values（log2intensity）and probe annotations were extracted from raw files downloaded from the Gene Expression Omnibus（GEO）database.Multiple probes mapped to a single gene（i.e.，unique Entrez gene ID）were collapsed as their medians.For the two remaining RNA-seq datasets，Liver Hepatocellular Carcinoma Project of The Cancer Genome Atlas（TCGA-LIHC）and Liver Cancer-RIKEN，JP Project from International Cancer Genome Consortium（ICGC LIRI-JP），we took the normalized read counts for log2transformation.Among the15 datasets，12 datasets contain both tumor and the adjacent normal samples，whereas only tumor samples are available for the three remaining datasets.Clinical information，such as tumor stages and survival time，was also collected if available.