| Resource | Description | Link |
|---|---|---|
| NAFLDkb (models) | Drug-discovery oriented knowledge base for NAFLD/MASLD. The models section catalogs in vitro and in vivo disease models manually curated from the literature (hepatocyte lines, primary cells, macrophages, stellate cells, animal models), annotated by category, class and species. | biosino.org/nafldkb/models |
| Liver Cell Atlas | Single-cell and single-nucleus atlas of human and mouse liver across health, obesity and steatotic disease, with browsable cell-type markers and spatial zonation. | livercellatlas.org |
| HCCDB | Integrative expression atlas of hepatocellular carcinoma assembling dozens of public HCC cohorts for cross-dataset gene-level and survival queries. | lifeome.net/database/hccdb |
| LiverTox | NIH knowledge base on drug-induced liver injury, with curated clinical and mechanistic records for individual compounds and herbals. | ncbi.nlm.nih.gov/books/NBK547852 |
KNOWLEDGE BASES
A curated set of public databases and knowledge bases we routinely use in the lab, grouped by topic. Links open in a new tab.
Liver and MASLD
Adipose tissue and metabolism
| Resource | Description | Link |
|---|---|---|
| Adipose Tissue Knowledge Portal | Central portal integrating clinical, transcriptomic and proteomic adipose data from >6,000 women and men across 67 datasets, covering multiple depots, resident cell types and adipocyte perturbation studies, down to single-cell resolution (Zhong, Cell Metab, 2025). | adiposetissue.org |
| Human Adipose Single-Cell Atlas | Single-nucleus atlas of human subcutaneous and visceral adipose tissue across BMI and sex, with the paired mouse dataset (Emont, Nature, 2022). | singlecell.broadinstitute.org (SCP1376) |
| GTEx Portal | Bulk expression and eQTL resource across 50+ human tissues, including subcutaneous and visceral adipose and liver; the reference for tissue-specific gene expression. | gtexportal.org |
| Type 2 Diabetes Knowledge Portal | Aggregated human genetics of type 2 diabetes and cardiometabolic traits (GWAS, effector genes, tissue-level annotations) with gene- and variant-centric views. | t2d.hugeamp.org |
| Adipocyte / brown fat MetaboLights datasets | EBI repository of metabolomics and lipidomics studies, including many adipose and hepatic lipid profiling datasets with raw files and metadata. | ebi.ac.uk/metabolights |
Single-cell and spatial transcriptomics
| Resource | Description | Link |
|---|---|---|
| CELLxGENE Discover | Standardized, cross-study collection of annotated single-cell datasets with interactive exploration and direct download of h5ad/rds objects. | cellxgene.cziscience.com |
| Human Cell Atlas Data Portal | Primary distribution point for Human Cell Atlas projects, with harmonized metadata and processed count matrices. | data.humancellatlas.org |
| Tabula Sapiens | Multi-organ single-cell reference from individual human donors, useful as a cross-tissue baseline for annotation. | tabula-sapiens.sf.czbiohub.org |
| Azimuth | Reference-based annotation service for single-cell data, mapping a query object onto curated tissue references. | azimuth.hubmapconsortium.org |
| CellMarker 2.0 | Manually curated catalog of cell-type marker genes for human and mouse tissues, including adipose and liver. | CellMarker 2.0 |
Genes, pathways and proteins
| Resource | Description | Link |
|---|---|---|
| MSigDB | Gene-set collections (hallmark, canonical pathways, GO, immunologic and cell-type signatures) underlying most GSEA and fgsea analyses. | gsea-msigdb.org |
| Reactome | Open, peer-reviewed pathway database with detailed reaction-level curation and pathway enrichment tools. | reactome.org |
| KEGG | Reference pathway maps for metabolism, signaling and disease; the standard vocabulary for metabolic pathway annotation. | genome.jp/kegg |
| STRING | Protein-protein association network integrating experimental, curated and predicted interactions, with built-in functional enrichment. | string-db.org |
| Human Protein Atlas | Tissue, single-cell, subcellular and pathology protein expression maps with immunohistochemistry images and survival associations. | proteinatlas.org |
Human genetics and variation
| Resource | Description | Link |
|---|---|---|
| gnomAD | Population allele frequencies from exome and genome sequencing of >800,000 individuals; the reference for variant rarity and constraint metrics. | gnomad.broadinstitute.org |
| GWAS Catalog | Curated repository of published genome-wide association studies, with harmonized summary statistics for most recent studies. | ebi.ac.uk/gwas |
| Open Targets Platform | Integrated gene-disease evidence for target identification and prioritization, combining genetics, expression, pathways and drug data. | platform.opentargets.org |
| ClinVar | Clinical interpretations of sequence variants and their relationships to disease, with submitter-level evidence. | ncbi.nlm.nih.gov/clinvar |
Omics repositories
| Resource | Description | Link |
|---|---|---|
| GEO | Largest public archive of functional genomics data (arrays, bulk and single-cell RNA-seq) with processed matrices and sample metadata. | ncbi.nlm.nih.gov/geo |
| ArrayExpress / BioStudies | EBI counterpart to GEO for functional genomics submissions, now served through BioStudies. | ebi.ac.uk/biostudies |
| SRA / ENA | Primary archives of raw sequencing reads; the starting point when a study's processed data are insufficient. | ebi.ac.uk/ena |
| PRIDE | Public repository for mass-spectrometry proteomics data, including raw spectra, identification results and quantification. | ebi.ac.uk/pride |
| Metabolomics Workbench | NIH repository of metabolomics studies with raw and processed data, plus tools for pathway mapping and cross-study comparison. | metabolomicsworkbench.org |