Reference: Kaur H et. al., (2019) Classification of early and late stage liver hepatocellular carcinoma
patients from their genomics and epigenomics profiles. PLoS One. 14(9):e0221476.
CancerLSP

CancerLSP is a web-bench Liver cancer stage prediction Server. It is developed to predict whether liver tissue samples is cancerous or normal and it also predict whether sample belong to Early (Stage-I) and Late stage of LIHC patients using gene expression data (derived from RNA-seq experiments in the form of RNA-Seq FPKM values) and Methylation Data (The methylation profiles acquired with the Illumina Human- Methylation450K DNA Analysis BeadChip assay, which is based on genotyping of bisulfite-converted genomic DNA at individual CpG-sites to provide a quantitative measure of DNA methylation in terms of Beta values). The user can also analyze data regarding expression of a gene in cancer or Normal and Early or late stage of LIHC for any gene among RNA transcripts included in this analysis.

Major features

Types of Data

  • Methylation Data

    The methylation profiles acquired with the Illumina Human- Methylation450K DNA Analysis BeadChip assay, which is based on genotyping of bisulfite-converted genomic DNA at individual CpG-sites to provide a quantitative measure of DNA methylation in terms of Beta values. The methylation value or beta values for a specific probe was calculated as the ratio M/(M + U), where M is the methylated signal intensity and U is the unmethylated signal intensity. 485,577 CpG methylation levels were measured across the genome

  • Gene Expression Data

    The sequencing platform of mRNA expression data is UNC_IlluminaHiseq_RNASeqV2. RNA expression in terms of FPKM values for 60,483 RNA transcripts are reported.