Technologic Platform with Databases Related to NRF2, Including Advanced Technologies and Bioinformatics Tools
This is an overview of databases and bioinformatics resources relevant to the NRF2 signaling pathway and its pharmacological modulation in noncommunicable diseases (NCDs).
| Database/tool name | Website address | Content | Use case (what can be done) | Open access Y/N | Species | Application Programming Interface (API) Y/N | Data access options |
|---|---|---|---|---|---|---|---|
| JASPAR | https://jaspar.elixir.no/ | transcription factor binding profiles | prediction of TF binding sites | Y | Arabidopsis thaliana, Caenorhabditis elegans, Ciona intestinalis, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, and Saccharomyces cerevisiae | Y | JASPAR downloads, JASPAR RESTful API, pyJASPAR, R Bioconductor Package |
| KEGG | https://www.genome.jp/kegg/ | Biological Pathways | Mapping of biological pathways | Y | Any | Y | Python, R Bioconductor (ggkegg) |
| IntAct | https://www.ebi.ac.uk/intact/home | Molecular interaction database and analysis | Deposit data and analysis tools for interaction data | Y | Any | Y | Can be used with Cytoscape App |
| ProteomeXchange | https://www.proteomexchange.org/ | Access to global proteomic data | Deposit and download proteomic data sets | Y | Any | ||
| PRIDE | https://www.ebi.ac.uk/pride/ | The proteomic database | Deposit and download proteomic data sets | Y | Any | Y | PRIDE Submission and Download Tools |
| g:Profiler | https://biit.cs.ut.ee/gprofiler/gost | Characterise and manipulate gene lists | Enrichment analysis | Y | +400 species | Y | Python, R (gprofiler2) |
| bio.tools | https://bio.tools/ | Registry of bioinformatics software and data resources | Info about software tools, databases, analysis | Y | Y | ||
| DAVID | https://davidbioinformatics.nih.gov/ | The Database for Annotation, Visualisation, and Integrated Discovery | Functional annotation tools for analysis of gene lists | Y | Any | Y | |
| Ensembl | https://www.ensembl.org/index.html | Genome Browser for vertebrate genomes | Comparative genomics, evolution, sequence variation and transcriptional regulation | Y | Vertebrates | Y | For small datasets use export option for more complex ones BioMart; R Bioconductor BiomaRt |
| cBioPortal | https://www.cbioportal.org/ | Cancer database | Access to cancer genomic data | Y | Human | Y | cBioPortal DataHub, R (cBioPortalData) |
| TCGA | https://portal.gdc.cancer.gov/ | Harmonised cancer sets | Access to clinical and cancer data | Y | |||
| UniProt | https://www.uniprot.org/ | Resource of protein sequence and functional information | Find homologies, alignment of protein sequences | Y | Any | Y | For small datasets use export option |
| The Human Protein Atlas | https://www.proteinatlas.org/ | All about human proteins | Expression and localisation data of human proteins and much more | Y | Human | N | Access single entries in different formats (XML, RDF, TSV or JSON) |
| UCSC Genome Browser | https://genome.ucsc.edu/ | Online and downloadable genome browser | Visualize genomic data | Y | Human and model organisms | Y | Various tools and options |
| Integrative Genomics Viewer | https://igv.org/ | Visualisation of genomic information | Interactive genome visualisation (Desktop App, Web App), Hi-C contact map viewer | Y | Any | N | Desktop App, Python, Web App |
| Cytoscape | https://cytoscape.org/ | Network Data Integration, Analysis and Visualization | Visualize protein-protein interaction network, disease-variant networks | Y | Any | N | Desktop App, R |
| DisGeNET | https://disgenet.com/ | Gene-disease association network | Knowledge database on human diseases | Y (partly) | Human | Y | R (disgenet2r), Cytoscape App |
| Sequence Read Archive | https://www.ncbi.nlm.nih.gov/sra | Repository for high-throughput sequencing data | Deposit and access sequencing data | Y | Any | N | SRA tools |
| BioGRID | https://thebiogrid.org/ | Database of Protein, Genetic and Chemical Interactions | Access to genetic and protein interaction data | Y | Human and model organisms | ||
| TFLink | https://tflink.net/ | transcription factor databases | transcription factor – target gene interactions, nucleotide sequences and genomic locations of transcription factor binding sites | Y | Mus musculus, Rattus norvegicus, Danio rerio, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae | N | Own Browser and Download options |
| Single cell atlas of the human retina | https://cellxgene.cziscience.com/collections/4c6eaf5c-6d57-4c76-b1e9-60df8c655f1e | Integrated multi-omics single cell atlas of the human retina | Evaluate expression levels at single cell resolution on Human retina | Y | Human | Y | |
| Human Peptide Atlas | https://peptideatlas.org/builds/human/ | a compendium of results from uniformly reprocessed mass spectrometry (MS) proteomics datasets. | Find how many and which peptides of the protein of interest have ever been identified in MS | Y | Human | ||
| Reactome | https://reactome.org/ | Pathway database | Organization of biological pathway information | Y | Any | Y | Browser, Python (reactome2py), R (ReactomeGSA) |
| STRING | https://string-db.org/ | Database of known and predicted protein-protein interactions. | Create protein-protein-interaction networks | Y | Any | Y | Browser, Cytoscape App |
| Comparative Toxicogenomics Database | https://ctdbase.org/ | How chemicals affect human health | e.g. identify proteins associated with chemicals | Y | Human | Y | Browser download and tools (e.g. Venn diagramme) |
Within the scope of BenBedPhar, the Ageing datasets contribute to understanding how NRF2-related mechanisms intersect with disease-specific pathways and clinical phenotypes. This integrated resource compiles approximately 51 entries from 0 biobank sources, representing collections from 0 countries. Sample matrices include a wide range of biological materials, which
collectively support translational analyses, biomarker discovery, and cross-disease comparison. By aligning this information under a harmonized structure, the Action strengthens its technological foundation for data-driven pharmacological innovation and facilitates coordination among research groups involved in preclinical and clinical NRF2 studies.