Dataset for the quantitative proteomics analysis of the primary hepatocellular carcinoma with single and multiple lesions

Abstract

Hepatocellular Carcinoma (HCC) is one of the most common malignant tumor, which is causing the second leading cancer-related death worldwide. The tumor tissues and the adjacent noncancerous tissues obtained from HCC patients with single and multiple lesions were quantified using iTRAQ. A total of 5513 proteins (FDR of 1%) were identified which correspond to roughly 27% of the total liver proteome. And 107 and 330 proteins were dysregulated in HCC tissue with multiple lesions (MC group) and HCC tissue with a single lesion (SC group), compared with their noncancerous tissue (MN and SN group) respectively. Bioinformatics analysis (GO, KEGG and IPA) allowed these data to be organized into distinct categories. The data accompanying the manuscript on this approach (Xing et al., J. Proteomics (2015), http://dx.doi.org/10.1016/j.jprot.2015.08.007[1]) have been deposited to the iProX with identifier IPX00037601.

Fig. 1

The qualities of the proteome dataset. (A) Frequency distribution of the identified proteins with ≥1 unique peptides. (B) Molecular weight distribution of identified proteins proved that there is no bias in the protein extraction process. (C) Isoelectric point distribution of the identified proteins to show the unbias of the protein extraction. (D) Protein hydrophobicity distribution of the identified proteins.

Fig. 2

The iTRAQ ratio distribution and involved biological processes of the differentially expressed proteins in the HCC with single and multiple lesions. (A) Volcano plot represented the protein abundance changes in the HCC cancerous tissue with multiple lesions comparing to their adjacent noncancerous tissues. A total of 107 dysregulated proteins with fold change ≥1.5 and p values <0.05 were identified. (B) Volcano plot represented the protein abundance changes in the HCC cancerous tissues with a single lesion comparing to their adjacent noncancerous tissue. A total of 330 dysregulated proteins with fold change ≥1.5 and p values <0.05 were identified. (C) Venn diagrams showed the overlaps and number of differentially expressed proteins in the HCC with single and multiple lesions. (D) GO analysis of the involved biological processes of the common dysregulated proteins in both types of the HCC. All of the biological processes were ranked in term of enrichment of the differentially expressed proteins, and the top 10 are presented here.

Fig. 3

The hierarchical clustering and involved biological processes analysis of differentially expressed proteins in the primary HCC with single and multiple lesions. (A) Hierarchical clustering of the 107 dysregulated proteins in the HCC with multiple lesions (MC vs. MN). (B) Hierarchical clustering of the 330 dysregulated proteins in the HCC with a single lesion (SC vs. SN). (C, D) GO analysis of the dysregulated proteins involved biological processes in the HCC with multiple lesions (C) and in the HCC with a single lesion (D).

Fig. 4

Gene ontology (GO) function analysis of differentially expressed proteins which is only dysregulated in HCC with a single lesion or HCC with multiple lesions. (A) GO analysis of the molecular function of the proteins which is only differentially expressed in HCC with multiple lesions. (B) GO analysis of the molecular function of the proteins which is only differentially expressed in HCC with a single lesion. (C) GO analysis of the cell component of the proteins which is only differentially expressed in HCC with multiple lesions. (D) GO analysis of the cell component of the proteins which is only differentially expressed in HCC with a single lesion. All of biological processes were ranked in term of the enrichment of the differentially expressed proteins, and the top 10 are presented.

Fig. 5

The key functions of the differentially expressed proteins involved in the HCC with single and multiple lesions according to IPA analysis. (A) Enriched Functions of the differentially expressed proteins that is only dysregulated in HCC with multiple lesions. (B) Enriched Functions of the differentially expressed proteins that is only dysregulated in HCC with a single lesion. All of pathways were ranked in term of the enrichment of the differentially expressed proteins, and the top 10 were presented.