Aquaculture Resilience Evidence Engine
Results to date
AREE re-examines public Pacific oyster gene-expression experiments to help researchers investigate how oysters respond to stress and what may contribute to survival, growth or recovery. It brings the results into a common format while keeping each experiment’s biological context and limitations. This page is rebuilt automatically every time results are pushed to main.
Last updated from commit 85863f6 (2026-10-17 18:54); site built 2026-10-18 01:54 UTC.
Browse real-study findings · Browse real evidence cards
Findings retain study-specific contrasts, gene descriptions, uncertainty and design limitations. They describe molecular associations, not validated predictors of resilience. The shared DECICOMP controls are not independent replication, and PRJNA735889’s tank-dependent analysis remains exploratory.
Counts distinguish public BioProjects from registered contrasts. PRJNA913164 contributes two contrasts with shared controls; neither the contrast count nor the BioProject count establishes independent replication.
How do expression findings relate to resilience? Learn what the comparison supports, why higher expression does not necessarily mean greater resilience, and what validation is needed.
What the work involves
For each experiment, we check which oysters were compared, recover the public RNA-sequencing data, estimate gene activity using a documented genome reference, and assess the quality of the samples and the experimental design. We then record expression differences, their uncertainty, and the reasons to treat a result cautiously. Some comparisons are withheld when treatment cannot be separated from parentage, developmental stage or inadequate replication.
The result is a resource for choosing follow-up experiments. A gene that changes after heat exposure may reflect protection, damage or both. Showing that it predicts survival requires independent animals with measured outcomes.
Reading the counts: A BioProject is a public dataset collection. A contrast is one treatment-versus-control comparison; a single project can supply several. An evidence record is one gene’s result in one comparison, including results without a statistically supported difference. Records are neither unique genes nor validated biomarkers. An evidence card collects available results for one displayed gene.
Read the biological overview · Understand the methods and terms
Real-study progress
| Study | BioProject | Stressor / phenotype | Analysis status | Links |
|---|---|---|---|---|
| CGIG_HEAT_RNASEQ_PRJNA516762 | PRJNA516762 | temperature / thermal_tolerance | raw reanalysis harmonized | design and limitations · paper · intake |
| CGIG_THERMOTOL_RNASEQ_PRJNA694496 | PRJNA694496 | temperature / thermal_tolerance | raw reanalysis harmonized | design and limitations · paper · intake · reanalysis |
| CGIG_OSHV1_RNASEQ_PRJNA1329250 | PRJNA1329250 | pathogen_challenge / immune_responsiveness | raw reanalysis harmonized | design and limitations · paper |
| CGIG_OA_RNASEQ_PRJNA826964 | PRJNA826964 | ocean_acidification_pH / metabolic_resilience | raw reanalysis harmonized | design and limitations |
| CGIG_SALINITY_RNASEQ_PRJNA756710 | PRJNA756710 | salinity / disease_susceptibility | raw reanalysis harmonized | design and limitations · paper |
| CGIG_OA_RNASEQ_PRJNA1196326 | PRJNA1196326 | ocean_acidification_pH / acidification_tolerance | raw reanalysis complete not harmonized | design and limitations |
| CGIG_STARVATION_RNASEQ_PRJEB86618 | PRJEB86618 | nutritional_limitation / disease_resistance | raw reanalysis harmonized | design and limitations · paper |
| CGIG_HAB_RNASEQ_PRJEB18614 | PRJEB18614 | harmful_algal_bloom_exposure / metabolic_resilience | raw reanalysis harmonized | design and limitations · paper |
| CGIG_OA_RNASEQ_PRJNA735889 | PRJNA735889 | ocean_acidification_pH / acidification_tolerance | raw reanalysis harmonized exploratory tank clustering unmodeled | design and limitations · paper |
| CGIG_HEAT_RNASEQ_PRJEB86646 | PRJEB86646 | temperature / disease_resistance | raw reanalysis harmonized | design and limitations · paper |
| CGIG_HEAT_RNASEQ_PRJNA913164 | PRJNA913164 | temperature / thermal_tolerance | raw reanalysis harmonized | design and limitations · paper |
| CGIG_MULTISTRESS_RNASEQ_PRJNA913164 | PRJNA913164 | multi_stressor_exposure / thermal_tolerance | raw reanalysis harmonized | design and limitations · paper |
| CGIG_OSHV1_RNASEQ_PRJNA593309 | PRJNA593309 | pathogen_challenge / immune_responsiveness | raw reanalysis harmonized | design and limitations · paper |
| CGIG_HEAT_RNASEQ_PRJNA593309 | PRJNA593309 | temperature / disease_resistance | raw reanalysis harmonized | design and limitations · paper |
| CGIG_TIRELEACHATE_RNASEQ_PRJNA856813 | PRJNA856813 | pollutant_exposure / metabolic_resilience | raw reanalysis harmonized | design and limitations · paper |
| CGIG_TIREPARTICLE_RNASEQ_PRJNA856813 | PRJNA856813 | pollutant_exposure / metabolic_resilience | raw reanalysis harmonized | design and limitations · paper |
| CGIG_VCRASSOSTREAE_RNASEQ_PRJNA515169 | PRJNA515169 | pathogen_challenge / immune_responsiveness | raw reanalysis harmonized | design and limitations · paper |
| CGIG_VTASMANIENSIS_RNASEQ_PRJNA515169 | PRJNA515169 | pathogen_challenge / immune_responsiveness | raw reanalysis harmonized | design and limitations · paper |
| CGIG_HEAT6H_RNASEQ_PRJNA407831 | PRJNA407831 | temperature / thermal_tolerance | raw reanalysis harmonized | design and limitations · paper |
| CGIG_HEAT24H_RNASEQ_PRJNA407831 | PRJNA407831 | temperature / thermal_tolerance | raw reanalysis harmonized | design and limitations · paper |
| CGIG_LARVAL_OA_RNASEQ_PRJNA298285 | PRJNA298285 | ocean_acidification_pH / acidification_tolerance | raw reanalysis harmonized | design and limitations |
| CGIG_LARVAL_HEAT_RNASEQ_PRJNA298285 | PRJNA298285 | temperature / thermal_tolerance | raw reanalysis complete not harmonized | design and limitations |
| CGIG_LARVAL_MULTISTRESS_RNASEQ_PRJNA298285 | PRJNA298285 | multi_stressor_exposure / larval_viability | raw reanalysis complete not harmonized | design and limitations |
| CGIG_PESTO_F0_RNASEQ_PRJEB58194 | PRJEB58194 | pollutant_exposure / larval_viability | raw reanalysis harmonized | design and limitations · paper |
| CGIG_PESTO_F1DIRECT_RNASEQ_PRJEB58194 | PRJEB58194 | pollutant_exposure / larval_viability | raw reanalysis harmonized | design and limitations · paper |
| CGIG_PESTO_F1PARENTAL_RNASEQ_PRJEB58194 | PRJEB58194 | pollutant_exposure / larval_viability | raw reanalysis complete not harmonized | design and limitations · paper |
| CGIG_HEAT37_RNASEQ_PRJNA1511593 | PRJNA1511593 | temperature / thermal_tolerance | raw reanalysis complete not harmonized | design and limitations |
| CGIG_HEAT42_RNASEQ_PRJNA1511593 | PRJNA1511593 | temperature / thermal_tolerance | raw reanalysis complete not harmonized | design and limitations |
| CGIG_VIBRIO12H_RNASEQ_PRJNA852380 | PRJNA852380 | pathogen_challenge / immune_responsiveness | raw reanalysis harmonized | design and limitations |
| CGIG_VIBRIO24H_RNASEQ_PRJNA852380 | PRJNA852380 | pathogen_challenge / immune_responsiveness | raw reanalysis harmonized | design and limitations |
| CGIG_HEAT12H_RNASEQ_PRJNA1244231 | PRJNA1244231 | temperature / thermal_tolerance | raw reanalysis complete not harmonized | design and limitations |
One displayed finding per harmonized study
| BioProject | Feature / real evidence card | Contrast | RefSeq description | Interpretation |
|---|---|---|---|---|
| PRJEB18614 | NCBI:GeneID:105339566 | alexandrium_minutum_vs_heterocapsa_triquetra_diet | dipeptidyl peptidase 1 | Study-level association; see design caveats |
| PRJNA407831 | NCBI:GeneID:105318591 | 35C_24h_vs_0h_gill | serine/threonine-protein kinase TBK1 | Study-level association; see design caveats |
| PRJNA407831 | NCBI:GeneID:105348305 | 35C_6h_vs_0h_gill | heat shock protein 68-like | Study-level association; see design caveats |
| PRJEB86646 | NCBI:GeneID:105327837 | 30C_vs_23C_fed_before_oshv1 | uncharacterized LOC105327837 | Study-level association; see design caveats |
| PRJNA516762 | NCBI:GeneID:117680673 | heat_35C_2h_vs_control_12C | heat shock protein 68 | Study-level association; see design caveats |
| PRJNA593309 | NCBI:GeneID:105336969 | 29C_vs_21C_12h_oshv1_cohabitation | uncharacterized LOC105336969 | Study-level association; see design caveats |
| PRJNA913164 | NCBI:GeneID:105329085 | 30C_seawater_vs_20C_adult_ctenidium | high mobility group-T protein | Study-level association; see design caveats |
| PRJNA298285 | NCBI:GeneID:105342907 | pH7.9_vs_pH8.1_20C_larvae | uncharacterized LOC105342907 | Study-level association; see design caveats |
| PRJNA913164 | NCBI:GeneID:105342400 | 30C_seawater_then_44C_emersion_6h_vs_20C_adult_ctenidium | serine/arginine-rich splicing factor 4 | Study-level association; see design caveats |
| PRJNA735889 | NCBI:GeneID:105321906 | ph_6.5_6.8_vs_ph_7.4_7.8_23d_juveniles | uncharacterized LOC105321906 | Exploratory; tank clustering unmodeled |
| PRJNA826964 | NCBI:GeneID:105346234 | ocean_acidification_vs_ambient_control | uncharacterized LOC105346234 | Study-level association; see design caveats |
| PRJNA1329250 | NCBI:GeneID:136276189 | oshv1_microvariant_challenge_vs_unchallenged_control | NFX1-type zinc finger-containing protein 1-like | Study-level association; see design caveats |
| PRJNA593309 | NCBI:GeneID:105343805 | oshv1_cohabitation_48h_vs_0h_21C | interferon regulatory factor 2 | Study-level association; see design caveats |
| PRJEB58194 | NCBI:GeneID:136270632 | pesticide_mixture_0_48hpf_vs_control_F0_gastrula_dlarva | cytochrome P450 2C14-like | Study-level association; see design caveats |
| PRJEB58194 | NCBI:GeneID:105321667 | pesticide_mixture_TE_vs_TT_F1_gastrula_pediveliger | uncharacterized LOC105321667 | Study-level association; see design caveats |
| PRJNA756710 | NCBI:GeneID:105321584 | low_salinity_10ppt_vs_30ppt_during_vibrio_infection | cysteine sulfinic acid decarboxylase | Study-level association; see design caveats |
| PRJEB86618 | NCBI:GeneID:105327731 | starved_vs_fed_ad_libitum_16d_before_oshv1 | serine protease inhibitor Cvsi-1 | Study-level association; see design caveats |
| PRJNA694496 | NCBI:GeneID:117686572 | thermotolerance_selected_vs_nonselected_control | sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1 | Study-level association; see design caveats |
| PRJNA856813 | NCBI:GeneID:105341503 | tire_leachate_high_vs_control_gill_day41 | double-stranded RNA-specific adenosine deaminase | Study-level association; see design caveats |
| PRJNA856813 | NCBI:GeneID:136276270 | tire_microparticles_high_vs_control_gill_day41 | ankyrin-1-like | Study-level association; see design caveats |
| PRJNA515169 | NCBI:GeneID:105321376 | vibrio_crassostreae_J2_9_vs_mock_injection_8h | EF-hand calcium-binding domain-containing protein 1 | Study-level association; see design caveats |
| PRJNA852380 | NCBI:GeneID:105318026 | vibrio_12h_vs_control_digestive_gland | tumor necrosis factor receptor superfamily member 11A | Study-level association; see design caveats |
| PRJNA852380 | NCBI:GeneID:105349013 | vibrio_24h_vs_control_digestive_gland | superoxide dismutase [Cu-Zn]-like | Study-level association; see design caveats |
| PRJNA515169 | NCBI:GeneID:105321376 | vibrio_tasmaniensis_LGP32_vs_mock_injection_8h | EF-hand calcium-binding domain-containing protein 1 | Study-level association; see design caveats |
Each row is the first finding from its own study’s selection; rows are ordered by study ID, not a global biomarker score. See all displayed findings and full-study downloads.
Workflow demonstration
The synthetic demo contains simulated studies, scores, meta-analysis and cards for testing the workflow. It is separate from the real findings above.
Recent activity
- 2026-10-17 ·
d315b39Add an in-browser query page over all harmonized evidence - 2026-10-17 ·
161078eClarify AREE findings and explain the workflow for biologists - 2026-10-10 ·
560e0cbRecord PRJNA1244231 gill heat contrast as reanalysed, not harmonized - 2026-10-10 ·
b543440Stage PRJNA1244231 (ERK inhibitor x heat, gill) for a genotype-first reanalysis - 2026-10-10 ·
7d96cd8Add the PRJNA852380 Vibrio 12 h and 24 h records to the evidence base - 2026-10-09 ·
7b458beStage PRJNA852380 (digestive-gland Vibrio time course) for a genotype-first reanalysis - 2026-10-09 ·
e6ad3ceRecord PRJNA1511593 gill heat contrasts as reanalysed but not harmonized - 2026-10-09 ·
9d2873aAdd the PESTO F0 and F1 direct-exposure records; record F1 parental as not harmonized - 2026-10-08 ·
a6e14c3Drop an unused loop variable in the PESTO test - 2026-10-08 ·
f08b92eCurate PRJEB58194 (PESTO pesticide mixture) as F0, F1-direct and F1-parental records - 2026-10-08 ·
837e901Add the PRJNA298285 larval acidification record; record warming as not harmonized - 2026-10-07 ·
2f4a4b5Curate PRJNA298285 (larval pH x temperature) as three larval records - 2026-10-07 ·
2c1639bAdd the PRJNA407831 6 h and 24 h heat records to the evidence base - 2026-10-06 ·
b7d0ef5Curate PRJNA407831 (Li 2018 tidal-origin heat stress) as 6 h and 24 h records - 2026-10-06 ·
537e6acAdd the PRJNA515169 virulent Vibrio records to the evidence base