Welcome to HCCsubtype!

Explore characterization of HCC molecular subtypes in LICA-FR cohort of 529 samples

HCCsubtype is a comprehensive web-based analysis tool based on LICA-FR cohort, a large, homogenous and well-annotated dataset for hepatocellular carcinoma (HCC). HCCsubtype has 4 embedded analysis modules: Genomic alteration analysis module, Transcriptomic/immune analysis module, Methylation profile analysis module and clinical feature correlation analysis module. HCCsubtype not only allows users to explore molecular and clinical characterization of each subtype, but also enables the comparison of a specific subtype with other subtypes or non-tumor liver.

To cite this paper:
Pan, L., Hirsch, TH., Fang, J., ..., Caruso S., Zucman-Rossi J. Integrated genomic analysis refines molecular subtypes of hepatocellular carcinoma. (2024) paper in submission

Updates: 01/04/2026
HCCsubtype release 1.0

Links for Other HCC datasets:

TCGA-LIHC (cBioPortal) | TCGA-LIHC (GDC) | CLCA (Chinese cohort) | PLANET (Singapore cohort)

Powered by Zucman lab (FunGest), Paris, 75006, France. 2023-2024. All rights reserved.

Summary of LICA-FR cohort information

Patient characteristics (461 patients)


Tumor characteristics (529 tumors)


*For patients with multiple etiologies, only keep the major one using the order 'HBV > HCV > Alcohol > NASH'

Explore mutational landscape in LICA-FR cohort (529 samples)

Explore the mutational spectrum of individual gene in LICA-FR cohort (529 samples)



Note: we use R package g3viz to generate the lollipop plot. Here, truncating class including frame_shift, nonsense, nonstop and splice_site; missense class including missense and silent.

Explore Copy-number alteration in LICA-FR cohort (529 samples)


Summary table of Copy-number alteration on each gene of interest in different groups

Here, homozygous deletion and amplification were focal CNA events (segment length <= 10 Mb, for details, see the method part in our corresponding paper).
Warning, summary table of CNA was generated using the readout of FACETS directly. Thus, there may be slight discrepancies comparing to the results from our paper after manual inspection. Download Frequency Plot Download Summary Plot Download Statistical Table

Explore RNAseq data in LICA-FR cohort (T: 406 samples, N: 51 samples)


Differential expression analysis in LICA-FR cohort (T: 406 samples, N: 51 samples)

Select the Case/Control subgroups for Comparison:


Method: Limma
Setting the threshold of differential expressed genes.

Volcano Plot of Differentially Expressed Genes
Heatmap for top 100 Differentially Expressed Genes
List of Differentially Expressed Genes

Explore Methylation profile in LICA-FR cohort (T: 260 samples, N: 35 samples)

Explore the correlation of clinical/molecular features and subtypes in LICA-FR cohort


Survival analysis in LICA-FR cohort with R0 resection



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Annotation of clinical and molecular features in LICA-FR cohort (529 HCC from 461 patients)

  • LICA_FR_annotation.xlsx

    • Mutation and Copy-number alteration data (116 WGS & 413 WES)

    Mutation data
  • Summary_of_driver_alterations_in_LICA_FR_cohorts.xlsx
  • Somatic_mutations_529s.RData
    • CNA data produced by FACETS pipeline
  • CNA_data_529s.RData

    • Methylation data (260 HCC & 35 NTL)

    Processed data by ChAMP R package
  • Processed_methylation_betaval_450K_295s.RData
  • Methylation_probe_annotation.RData
    • Initial data
  • Methylation_Pvalue_295s.RData
  • Methylation_Bval_295s.RData
  • Methylation_data_project.xlsx

    • Transcriptome data (406 HCC & 51 NTL)

    Expression Matrix
  • RNAseq_count_457s.RData
  • RNAseq_vst_457s.RData
  • RNAseq_tpm_457s.RData
  • RNAseq_fpkm_457s.RData
  • RNAseq_gene_table.RData
  • Pathway_enrichment_score_msigdbr.RData
    • Immune score
  • MCPcounter_Becht_457s.RData
  • MCPcounter_Danaher_457s.RData

    • RPPA data (181 HCC & 25 NTL)

  • RPPA_normalized_matrix_206s.xlsx
  • RPPA_antibody_list.xlsx

    • Contact us

    For any questions about this data portal, please contact us


    Long Pan, MD, PhD student

    E-mail: long.pan@inserm.fr

    Sandrine Imbeaud, PhD

    E-mail: sandrine.imbeaud@inserm.fr

    Theo Hirsch, PhD

    E-mail: theo.hirsch@inserm.fr

    Cordeliers Research Center
    Inserm UMRS1138 – Team 28
    FunGeST - Functional Genomics of Solid Tumors
    Sorbonne Université - Université Paris Cité

    Citation

    Please cite the following publication:
    Pan, L., Hirsch, TH., Fang, J., ..., Caruso S., Zucman-Rossi J.. Integrated genomic analysis refines molecular subtypes of hepatocellular carcinoma. (2024) paper in submission



    Note, only the geographic location of users are collected to summarise the distribution of users in the world.