Human Gene Set: REQUENA_FIBROLAMELLAR_CARCINOMA_MARKERS_UP


Standard name REQUENA_FIBROLAMELLAR_CARCINOMA_MARKERS_UP
Systematic name M51095
Brief description Genes consistenly up-regulated in Fibrolamellar Hepatocellular Carcinoma across independent datasets.
Full description or abstract Fibrolamellar carcinoma (FLC) is a liver cancer of adolescents and young adults characterized by increased PKA activity. We performed a multi-omics study of 1,412 tumor-normal paired liver samples from cohorts of patients with FLC, hepatoblastoma (HBL), intrahepatic cholangiocarcinoma (iCCA), and hepatocellular carcinoma (HCC), including ribosomal RNA-depleted whole-transcriptome RNA-seq samples sequenced on Illumina NextSeq and HiSeq platforms. Using differential expression analysis, we identified genes with a consistent variation trend across samples, defining the fibrolamellar carcinoma signature, hepatoblastoma signature, hepatocellular carcinoma signature, and the intrahepatic cholangiocarcinoma signature. Comparing these transcriptomic gene signatures, we identified genes consistently upregulated only in the FLC signature and not in the other signatures. The top 35 genes with the largest fold changes and 100% consistency were designated as the fibrolamellar carcinoma markers up. Pathway enrichment analysis using GSEA, PADOG, and CAMERA confirmed that this gene set is consistently enriched across FLC datasets, but not in HBL, iCCA, or HCC.
Collection C2: Curated
      CGP: Chemical and Genetic Perturbations
Source publication Pubmed 39738196   Authors: Requena D,Medico JA,Soto-Ugaldi LF,Shirani M,Saltsman JA 3rd,Torbenson MS,Coffino P,Simon SM
Exact source Supplementary Table 3. Transcriptomic FLC Signature. dbGAP accession: phs003643.v1.p1
Related gene sets (show 4 additional gene sets from the source publication)
External links https://fibrolamellardatabase.org
Filtered by similarity ?
Source species Homo sapiens
Contributed by David Requena (The Rockefeller University)
Source platform or
identifier namespace		 Human_Ensembl_Gene_ID
Dataset references  
Download gene set format: grp | gmt | xml | json | TSV metadata
Compute overlaps ? (show collections to investigate for overlap with this gene set)
Compendia expression profiles ? NG-CHM interactive heatmaps
(Please note that clustering takes a few seconds)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)

Legacy heatmaps (PNG)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)
Advanced query Further investigate these 35 genes
Gene families ? Categorize these 35 genes by gene family
Show members (show 35 source identifiers mapped to 35 genes)
Version history 2026.2.Hs: First Introduced.


Creative Commons Attribution 4.0 International License (CC-BY-4.0)

The contents of this gene set are protected by copyright (c) 2004-2026 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California, subject to the terms and conditions of the Creative Commons Attribution 4.0 International License.

See the full MSigDB license terms here.