(4) The chromosome locations of DEGs.

(5) Functional annotation of DEGs.

(6) Exon expression level analysis.

(7) Identification of novel DE exon-exon junctions.

The key study results:

(1) For the first time the RNA-seq analysis of HBV-related HCC.

(2) 1,378 significantly DEGs and 24, 338 DEEs were identified.

(3) 54 bio-function terms and 41 canonical pathways related to HCC.

(4) Many of chromosomal aberrations were identified, especially 8q24.

(5) Some splicing patterns were identified.

(6) A novel-splicing variant in ATAD2 was identified.

Conclusion:

Overall, by RNA-seq our study represents the most comprehensive

characterization of the HBV-related HCC transcriptome including gene

level expression changes, exon level expression changes and novel splicing

variants, which provided important clues for understanding the molecular

mechanisms of HCC pathogenesis at system-wide levels.

Key words：next-generation sequencing; liver cancer; transcriptome,

Hepatitis B virus; exon