Biomarker Database
This database compiles candidate resilience biomarkers discovered across shellfish genomic studies. Biomarkers are searchable by species, condition, trait, discovery class, and evidence type. Use the search bar and column sort features to explore entries, and download the full or filtered dataset using the buttons below. To suggest additions or provide feedback, use the Feedback / Request Update link.
- Search: Use the search box (top right) to query any text across all columns.
- Sort: Click any column header to sort the table by that column.
- Filter: Use the dropdown filters above each column to narrow results by species, condition, class, etc.
- Download: Use the CSV, Excel, or Copy buttons to download the current (filtered) view.
- Feedback: Use the Feedback / Request Update link to suggest a new biomarker entry or report an issue.
Download Full Database (CSV) Feedback / Request Update
| ID | Gene Name | Species | Condition | Trait | Effect | Class | Evidence | Source | Rank |
|---|---|---|---|---|---|---|---|---|---|
| BM001 | HSP70 | Crassostrea gigas | Thermal Stress | Thermotolerance | Upregulated | Genomic Feature | Species-specific | Arredondo-Espinoza et al. 2023 (https://doi.org/10.1016/j.cbd.2023.101089) | 3 |
| BM002 | HSP90 | Crassostrea gigas | Thermal Stress | Thermotolerance | Upregulated | Genomic Feature | Cross-species | Arredondo-Espinoza et al. 2023 (https://doi.org/10.1016/j.cbd.2023.101089) | 4 |
| BM003 | HSPA5 | Crassostrea virginica | Perkinsus marinus Infection | Infection Tolerance | Upregulated | Genomic Feature | Species-specific | Proestou et al. 2023 (https://doi.org/10.3389/fgene.2023.1054558) | 3 |
| BM004 | SOD1 | Crassostrea virginica | Perkinsus marinus Infection | Infection Tolerance | Upregulated | Genomic Feature | Cross-species | Proestou et al. 2023 (https://doi.org/10.3389/fgene.2023.1054558); Chan et al. 2021 (https://doi.org/10.3389/fgene.2021.795706) | 5 |
| BM005 | CAT | Crassostrea virginica | Perkinsus marinus Infection | Infection Sensitivity | Downregulated | Genomic Feature | Species-specific | Johnson et al. 2020 (https://doi.org/10.3389/fmars.2020.00598) | 2 |
| BM006 | IL-17 | Crassostrea gigas | Perkinsus marinus Infection | Infection Tolerance | Upregulated | Protein Interaction Network | Cross-species | Chan et al. 2021 (https://doi.org/10.3389/fgene.2021.795706) | 4 |
| BM007 | TLR | Crassostrea virginica | Perkinsus marinus Infection | Infection Sensitivity | Downregulated | Protein Interaction Network | Species-specific | Sullivan and Proestou 2021 (https://doi.org/10.1016/j.aquaculture.2021.736831) | 3 |
| BM008 | DNMT3 | Crassostrea virginica | Ocean Acidification | Resilience | Upregulated | Genomic Feature | Species-specific | Roberts et al. unpublished (https://github.com/sr320/ceasmallr) | 2 |
| BM009 | NF-kB | Crassostrea virginica | Perkinsus marinus Infection | Infection Sensitivity | Upregulated | Protein Interaction Network | Cross-species | Johnson et al. 2020 (https://doi.org/10.3389/fmars.2020.00598); Proestou and Sullivan 2020 (https://doi.org/10.1016/j.fsi.2019.12.001) | 4 |
| BM010 | TIMP | Crassostrea virginica | Perkinsus marinus Infection | Infection Tolerance | Upregulated | Ontology Enrichment | Species-specific | Proestou and Sullivan 2020 (https://doi.org/10.1016/j.fsi.2019.12.001) | 2 |
| BM011 | MMP | Crassostrea virginica | Perkinsus marinus Infection | Infection Sensitivity | Upregulated | Ontology Enrichment | Cross-species | Sullivan and Proestou 2021 (https://doi.org/10.1016/j.aquaculture.2021.736831); Proestou and Sullivan 2020 (https://doi.org/10.1016/j.fsi.2019.12.001) | 4 |
| BM012 | PRDX | Crassostrea gigas | Thermal Stress | Thermotolerance | Upregulated | Genomic Feature | Cross-species | Arredondo-Espinoza et al. 2023 (https://doi.org/10.1016/j.cbd.2023.101089) | 3 |
| BM013 | GPx | Crassostrea virginica | Ocean Acidification | Resilience | Upregulated | Genomic Feature | Species-specific | Roberts et al. unpublished (https://github.com/sr320/ceasmallr) | 2 |
| BM014 | CLEC | Crassostrea virginica | Perkinsus marinus Infection | Infection Tolerance | Upregulated | Protein Interaction Network | Cross-species | Chan et al. 2021 (https://doi.org/10.3389/fgene.2021.795706); Proestou et al. 2023 (https://doi.org/10.3389/fgene.2023.1054558) | 5 |
| BM016 | FTH1 | Crassostrea gigas | Thermal Stress | Thermotolerance | Upregulated | Ontology Enrichment | Species-specific | Arredondo-Espinoza et al. 2023 (https://doi.org/10.1016/j.cbd.2023.101089) | 2 |
Column descriptions: Class — discovery class: Genomic Feature, Ontology Enrichment, or Protein Interaction Network. Evidence — Species-specific (identified in one species) or Cross-species (identified across multiple species). Rank — confidence score (1–5) based on the number of supporting studies, species, and data types; higher scores indicate stronger evidence. Source — publication(s) providing original evidence.
Database hosted on GitHub. Stable annual releases are made to ensure data, webpage, and software are up to date. To contribute data or join as a collaborator, open a GitHub Issue.