A static, client-side bioinformatics tool for cross-species gene analysis in Fusarium.
geneRelate enables researchers to map orthologs, explore protein-protein interactions, perform functional enrichment analysis, and visualize phylogenetic gene trees across 20 Fusarium species — entirely in the browser with no backend server required.
A live demo can be accessed through the link in the repository description.
- Cross-Species Ortholog Mapping — Identify orthologs across 20 Fusarium species using phylogeny-based NOG assignments from STRING/eggNOG, with alias-based name matching as fallback
- Protein-Protein Interaction (PPI) Tables — Browse interactions from STRING v12.0 with configurable score thresholds (400–999)
- Interactive PPI Network — Force-directed network visualization with zoom, pan, and drag. Hub genes identified by degree centrality
- GO Annotations — Per-gene Gene Ontology terms (Biological Process, Molecular Function, Cellular Component)
- KEGG Pathway Annotations — Per-gene KEGG pathway mappings
- GO Enrichment Analysis — Over-representation analysis using Fisher's Exact Test (hypergeometric) with Benjamini-Hochberg FDR correction
- KEGG Enrichment Analysis — Pathway enrichment with the same statistical framework
- Publication-Quality Plots — Bar charts, dot plots, and hierarchical clustering dendrograms with 7 color palettes (Default, Viridis, Magma, Plasma, Blues, Reds, Greys)
- Hierarchical Clustering Tree — UPGMA dendrogram clustering enriched terms by gene set overlap (Jaccard distance), similar to ShinyGO's Tree view
- Interactive Gene Tooltips — Hover over any gene or protein ID in tables, network nodes, or phylogeny tree leaves to see functional annotation, GO terms, KEGG pathways, and direct links to UniProt, STRING, AmiGO, KEGG, and eggNOG
- Phylogeny Analysis — Per-gene phylogenetic trees from eggNOG v7 pre-computed protein family trees, mapped via STRING orthologous groups at the Fungi level. Query genes are highlighted in red and target species in blue, with interactive tooltips on each leaf node
- Phylogenetic Export Formats — Newick, NEXUS (PAUP*, MrBayes, FigTree), and PhyloXML (Archaeopteryx, ETE, forester) for compatibility with external phylogenetic analysis tools
- Multiple Export Formats — CSV, PNG (high-resolution), SVG, and PDF
- Dark / Light Theme — Persistent theme preference
geneRelate includes data for 20 Fusarium species sourced from STRING v12.0:
| Species | Taxon ID | Notes |
|---|---|---|
| F. graminearum PH-1 | 229533 | |
| F. verticillioides 7600 | 334819 | |
| F. oxysporum f. sp. lycopersici 4287 | 426428 | |
| F. oxysporum Fo5176 | 660025 | |
| F. fujikuroi IMI 58289 | 1279085 | |
| F. sporotrichioides | 5514 | |
| F. poae | 36050 | |
| F. nygamai | 42673 | |
| F. venenatum | 56646 | |
| F. oxysporum f. sp. radicis-cucumerinum | 327505 | |
| F. oxysporum f. sp. cubense race 1 | 1229664 | |
| F. oxysporum f. sp. cubense race 4 | 1229665 | |
| F. longipes | 694270 | |
| F. kuroshium | 2010991 | |
| F. fasciculatum | 2594813 | |
| F. sp. AF-4 | 1325735 | |
| F. sp. AF-6 | 1325737 | |
| F. sp. AF-8 | 1325734 | |
| F. culmorum | 5516 | Synthetic (derived from F. graminearum) |
| F. pseudograminearum CS3096 | 1028729 | Synthetic (derived from F. graminearum) |
Cross-species ortholog identification uses a two-tier approach:
- Primary — NOG-based orthology: Each protein's eggNOG orthologous group (NOG) assignment is obtained from STRING v12.0 at the Fungi level (taxid 4751). Proteins sharing the same NOG ID are orthologs. This is phylogeny-based orthology derived from eggNOG's species tree reconciliation and maximum-likelihood methods.
- Fallback — Alias matching: For genes without NOG assignments, cross-species mapping falls back to name/alias matching using pre-computed lookup tables from FungiDB and Ensembl Fungi.
Results are labeled by match type ("Ortholog" vs "Alias") so users can assess confidence. Gene resolution supports protein IDs, locus tags, preferred names, and aliases (case-insensitive).
Interaction data is sourced from STRING v12.0. The network visualization uses a synchronous force-directed layout (300 iterations) to cluster related proteins. Hub genes are identified based on degree centrality (top 20%, minimum degree 3).
GO and KEGG enrichment is performed using a Fisher's Exact Test (hypergeometric test) with Benjamini-Hochberg FDR correction. Background sets are species-specific genome-wide annotations.
Enriched terms can be visualized as a hierarchical clustering dendrogram (Tree view). The clustering method:
- Distance metric — Pairwise Jaccard distance between terms based on their annotated gene sets: d(A, B) = 1 − |A ∩ B| / |A ∪ B|. Terms sharing more genes are closer in the tree.
- Clustering algorithm — UPGMA (Unweighted Pair Group Method with Arithmetic Mean), which produces ultrametric trees where the distance from the root to any leaf is equal. This is appropriate for functional term clustering where the goal is to identify groups of related biological processes, not to infer evolutionary relationships.
- Visualization — Horizontal dendrogram with branch length proportional to Jaccard distance. Leaf nodes are colored by significance (−log₁₀ FDR) using the selected color palette.
Gene trees are derived from eggNOG v7 pre-computed protein family phylogenies (Hernández-Plaza et al., 2026). Orthologous group (NOG) assignments are obtained from STRING v12.0 hierarchical orthology data. The mapping pipeline:
- For each protein, STRING provides eggNOG NOG assignments at the Fungi level (taxid 4751)
- Proteins sharing the same NOG ID are grouped into orthogroups
- eggNOG v7 protein family trees are filtered for families with Fungi-level OGs
- STRING protein IDs are matched directly against eggNOG v7 tree tip labels (both use
taxid.UniProtIDformat)
Trees are rendered as rectangular cladograms with query genes highlighted in red and target species genes highlighted in blue. Hovering over any leaf node shows species name, gene IDs, orthogroup, branch length, and links to eggNOG, STRING, and UniProt. Export is available in PNG, SVG, PDF, Newick, NEXUS, and PhyloXML formats.
F. culmorum and F. pseudograminearum are not available in STRING. Their data is derived from F. graminearum via gene ID prefix mapping (FGSG_ → FCUL_ / FPSE_). PPI networks, GO annotations, and KEGG pathways shown for these species reflect F. graminearum data and should be interpreted accordingly.
| Database | Version | URL |
|---|---|---|
| STRING | v12.0 | https://string-db.org |
| KEGG | Current | https://www.kegg.jp |
| Gene Ontology | Current | https://geneontology.org |
| eggNOG | v7 | https://eggnogdb.org |
| FungiDB / VEuPathDB | Current | https://fungidb.org |
- Orthology coverage — NOG-based ortholog mapping covers genes with STRING/eggNOG Fungi-level assignments. Genes without NOG assignments fall back to alias-based name matching, which may miss orthologs with different names or produce false matches.
- Synthetic species — F. culmorum and F. pseudograminearum data assumes 1:1 correspondence with F. graminearum, which is not guaranteed biologically.
- KEGG coverage — Only species with KEGG organism codes have pathway data. Some species will show zero KEGG annotations.
- Static data — Pre-downloaded data does not auto-update. Periodic pipeline re-runs are needed when source databases release new versions.
- Select a source species from the dropdown (or let auto-detection identify it from gene prefixes)
- Enter gene names (one per line or comma-separated) — supports locus tags (e.g.,
FGSG_00362), gene names (e.g.,TRI5), or protein IDs - Optionally select target species for cross-species ortholog lookup
- Adjust the PPI score threshold (default: 700)
- Click Analyze
geneRelate is a fully static site. To run locally:
# Any static file server works
cd public
python -m http.server 8000
# or
npx serve .Then open http://localhost:8000 in your browser.
- Szklarczyk, D., et al. (2023). The STRING database in 2023. Nucleic Acids Research, 51(D1), D483–D489. https://doi.org/10.1093/nar/gkac1000
- Kanehisa, M., et al. (2023). KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Research, 51(D1), D587–D592. https://doi.org/10.1093/nar/gkac963
- The Gene Ontology Consortium. (2023). The Gene Ontology knowledgebase in 2023. Genetics, 224(1), iyad031. https://doi.org/10.1093/genetics/iyad031
- Amos, B., et al. (2022). VEuPathDB: The eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Research, 50(D1), D898–D911. https://doi.org/10.1093/nar/gkab929
- Hernández-Plaza, A., et al. (2026). eggNOG v7: phylogeny-based orthology predictions and functional annotations. Nucleic Acids Research, 54(D1), D402. https://doi.org/10.1093/nar/gkaf1249