Plasma cell‐free transcriptome profiling in blood plasma from chronic liver disease patients

Supplementary data associated with the data descriptor with title: "Plasma cell‐free transcriptome profiling in blood plasma from chronic liver disease patients"

File description:

Analyses_results_summary.xlsx: Overview of results showed in the technical validation section. A summary of the contents can be found in the “summary” tab in the file

annotation_cohort1.csv: laboratory and clinical annotation of samples/patients belonging to cohort 1.

annotation_cohort2.csv: laboratory and clinical annotation of samples/patients belonging to cohort 2.

CodeBook_ann_cohort1.xlsx: extended description of variables included in the cohort 1 annotation. 

CodeBook_ann_cohort2.xlsx: extended description of variables included in the cohort 2 annotation. 

circRNA_diffexpr.csv: differential abundance analysis of circRNA results, includes detected circRNA with p adjusted < 0.05 and abs(logFC) > 2.

hepatocyte_signature_deconvolution.csv: results of the vector regression to deconvolve cell types of origin within the plasma cell-free transcriptome.

Figure 4. Gene set enrichment and cellular signatures in NAFLD vs. no NAFLD (cohort 1).(a) Gene set enrichment analysis (GSEA) using GO and Hallmark databases (|NES| > 1, FDR < 0.25). (b) Hepatocyte-specific gene expression (CPM counts, left) and singscore-derived hepatocyte signature (right). (c) Volcano plot of differentially expressed circRNAs (|log2FC| > 2, p < 0.05), identifying 97 dysregulated circRNAs.  Significance levels: *p < 0.05, **p < 0.01, ***p < 0.001.

Figure 5. Gene set enrichment and cellular signature analysis in cirrhosis vs absence of cirrhosis (cohort 1). (a) Gene set enrichment analysis (GSEA) using GO and Hallmark databases (|NES| > 1, FDR < 0.25). (b) Hepatocyte-specific gene expression (CPM counts, left) and singscore-derived hepatocyte signature (right).  (c) Volcano plot showing the differential expression of circRNAs. Statistical significance is indicated as *p < 0.05, **p < 0.01, and ***p < 0.001.

Figure 6. Gene set enrichment and cellular signatures in high vs. low fibrosis (cohort 2). (a) Gene set enrichment analysis (GSEA) using GO and Hallmark databases(|NES| > 1, FDR < 0.25). (b) Hepatocyte-specific gene expression (CPM counts, left) and singscore-derived hepatocyte signature (right).  (c) Deconvolution analysis showing proportions of neutrophils, NK cells, B cells, and platelets. Significance levels: *p < 0.05, **p < 0.01, ***p < 0.001. 

Figure 7. Gene set enrichment and cellular signatures in NASH patients at risk of HCC progression (cohort 2). (a) Gene set enrichment analysis (GSEA) using GO and Hallmark databases. (|NES| > 1, FDR < 0.25). (b) Hepatocyte-specific gene expression (CPM counts, left) and singscore-derived hepatocyte signature (right). (c) Deconvolution analysis showing proportions of neutrophils, goblet cells, B cells, and platelets. Significance levels: *p < 0.05, **p < 0.01, ***p < 0.001.

Total_RNA_description.pdf: text describing the findings of the Gene set enrichment, hepatocyte signature, circRNA analyses.  

DAA_August_2025.doc: data access agreement to be signed in order to request access to the dataset deposited in the EGA repository

DTA_UGent_August 2025.docx: data transfer agreement (EU countries) to be signed together with the DAA in order to request access to the dataset deposited in the EGA repository

DTA_UGent_non-EU country_August 2025.docx: additionall data transfer agreement for non-EU countries to be signed together with the DAA and standard DTA in order to request access to the dataset deposited in the EGA repository

For instructions to reproduce the results in the publication check the github repository:  https://github.com/OncoRNALab/GCP_exRNA_liver.git