Extended Data Fig. 1: Overview of multi-omics landscape of HBV-related early-stage HCC and quality control for the mass spectrometry platform. | Nature

Extended Data Fig. 1: Overview of multi-omics landscape of HBV-related early-stage HCC and quality control for the mass spectrometry platform.

From: Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma

Extended Data Fig. 1

a, Schematic of the multi-omics analyses of HBV-related early-stage HCC. The number of proteins, phosphorylation sites, expressed genes and genomic mutations identified in the proteome, phospho-proteome, transcriptome and whole-genome sequencing (WGS) data are displayed on the right of the middle panel. b, Illustration of 110 paired HCC cases used in the individual omics experiments. The proteome, phospho-proteome, genome and transcriptome experiments are coloured red, orange, blue and green, respectively. For each omics dataset, the top panel represents the non-tumour tissues and the bottom panel represents the tumour tissues. c, Longitudinal quality control of mass spectrometry using tryptic digest of HEK293T cells. The bottom-left half of the panel represents the pairwise Spearman’s correlation coefficients of the samples, and the top-right half of the panel depicts the pairwise scatter plots from the same comparison. d, Scatter plots and Spearman’s correlation coefficients for replicate proteome profiling of six HCC samples (three paired tumour and non-tumour samples). The x and y axes represent the log2-transformed protein intensities in each pairwise comparison. Notably, repeat experiments with the same samples have good reproducibility, with a high level of correlation (average, 0.9; range, 0.88–0.92).

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