Real-study findings
Findings are reported within each study. For inference-eligible studies, up to ten genes are selected from adjusted p < 0.05, ordered by adjusted p-value, then absolute effect and feature ID. For exploratory PRJNA735889, ten descriptive effects are ordered by absolute effect; nominal FDR is not used for selection. These are browsing selections, not global biomarker rankings. Full harmonized tables are linked for every available study. No cross-study effect pooling is presented because matching effect scales and broad phenotype labels alone do not establish comparable contrasts.
How do expression findings relate to resilience? Differential expression identifies molecular differences; linking them to survival, performance or recovery requires outcome evidence and independent validation. Higher expression does not necessarily mean greater resilience.
Guide to effect sizes, uncertainty and gene descriptions.
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PRJEB18614 — harmful algal bloom exposure
Study design, replication and limitations
A. minutum exposure is unfavorable. The publication reports remodelling of the gill cycling transcriptome (loss of oscillations, de novo oscillating transcripts, shortened periods) and toxin accumulation, not survival. AREE records the time-averaged gill transcriptional response to the toxic diet.
Records: 25,045; genes with nonmissing raw p-values: 25,045. Study-level associations.
Adjusted p < 0.05: 6,980 (3,690 positive, 3,290 negative). Counts are study-level molecular associations.
Biological replication: 24 pooled RNA-seq libraries in the primary analysis (12 per diet), each pooling gill RNA from 6 oysters. The original 26 libraries cover 13 time-matched pairs; both day 2 ZT 8.5 pools are excluded, leaving 12 pairs. There is no replication within a diet-by-time cell. Each diet used three tanks; sample_size counts analysed pools, not individual oysters or independent tanks.
Treatment: Continuous feeding on the paralytic shellfish toxin-producing dinoflagellate Alexandrium minutum (strain AM89BM) at about 400 cells/mL, mimicking a bloom
Control: Continuous feeding on the non-toxic dinoflagellate Heterocapsa triquetra, sampled at the same times
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
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| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105339566 | dipeptidyl peptidase 1 | log2 fold change | 1.512 | 0.04179 | 1.988e-282 | Study-level association; see design caveats |
| NCBI:GeneID:105348980 | solute carrier family 15 member 4 | log2 fold change | 1.766 | 0.05881 | 3.635e-194 | Study-level association; see design caveats |
| NCBI:GeneID:117685091 | uncharacterized LOC117685091 | log2 fold change | 3.402 | 0.1173 | 5.323e-181 | Study-level association; see design caveats |
| NCBI:GeneID:105338718 | lysosome-associated membrane glycoprotein 1 | log2 fold change | 0.9974 | 0.03559 | 4.589e-169 | Study-level association; see design caveats |
| NCBI:GeneID:117687818 | uncharacterized LOC117687818 | log2 fold change | 3.059 | 0.1133 | 7.313e-157 | Study-level association; see design caveats |
| NCBI:GeneID:105342870 | ATP-dependent translocase ABCB1 | log2 fold change | 3.656 | 0.1369 | 1.263e-153 | Study-level association; see design caveats |
| NCBI:GeneID:105345248 | CD63 antigen | log2 fold change | 1.1 | 0.04353 | 2.917e-137 | Study-level association; see design caveats |
| NCBI:GeneID:105346410 | arylacetamide deacetylase | log2 fold change | 2.32 | 0.09382 | 1.426e-131 | Study-level association; see design caveats |
| NCBI:GeneID:105337461 | maestro heat-like repeat-containing protein family member 1 | log2 fold change | 1.287 | 0.0529 | 2.093e-127 | Study-level association; see design caveats |
| NCBI:GeneID:105322438 | glycosylated lysosomal membrane protein | log2 fold change | 1.309 | 0.05413 | 6.91e-126 | Study-level association; see design caveats |
PRJNA1244231 — temperature
Study design, replication and limitations
No phenotype is deposited and no publication is linked; AREE records the gill transcriptional response to acute heat.
Not harmonized. Study-level descriptive work exists, but the design does not support the released inferential evidence table. See the study limitations.
PRJNA407831 — temperature
Study design, replication and limitations
Intertidal-origin F1 oysters showed higher survival after acute heat stress (42 C, 1 h) and higher metabolic rates at 35 C than subtidal-origin oysters, with slower growth, and more transcriptional plasticity. AREE records the gill transcriptional response to 35 C averaged over the four populations, not survival per library.
Records: 23,282; genes with nonmissing raw p-values: 23,202. Study-level associations.
Adjusted p < 0.05: 2,714 (1,363 positive, 1,351 negative). Counts are study-level molecular associations.
Biological replication: 23 libraries analysed (24 sequenced; one 0 h outlier left out): 11 at 0 h and 12 at 24 h. Each library pools equal gill RNA from five oysters of one culture tank; four populations (two sites x intertidal or subtidal origin) x three tanks, and the same tanks are sampled at each time.
Treatment: Held in 35 C seawater (sublethal) for 24 h
Control: Same tanks sampled at 0 h, before the temperature was raised (laboratory acclimation 14.2-18.2 C)
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
Download all harmonized evidence
| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105318591 | serine/threonine-protein kinase TBK1 | log2 fold change | -1.379 | 0.08597 | 1.442e-53 | Study-level association; see design caveats |
| NCBI:GeneID:105346591 | kelch-like protein 18 | log2 fold change | -0.8873 | 0.06585 | 2.307e-37 | Study-level association; see design caveats |
| NCBI:GeneID:117690579 | small nucleolar RNA U3 | log2 fold change | 6.177 | 0.469 | 9.356e-36 | Study-level association; see design caveats |
| NCBI:GeneID:105348305 | heat shock protein 68-like | log2 fold change | 7.593 | 0.5948 | 1.367e-33 | Study-level association; see design caveats |
| NCBI:GeneID:105321326 | endoplasmic reticulum membrane sensor NFE2L1 | log2 fold change | -2.458 | 0.2017 | 1.584e-30 | Study-level association; see design caveats |
| NCBI:GeneID:105334510 | heat shock protein 68-like | log2 fold change | 7.57 | 0.6373 | 5.576e-29 | Study-level association; see design caveats |
| NCBI:GeneID:105334580 | BAG family molecular chaperone regulator 3 | log2 fold change | 5.623 | 0.4848 | 1.282e-27 | Study-level association; see design caveats |
| NCBI:GeneID:105331925 | serine/threonine-protein kinase PRP4 homolog | log2 fold change | 0.6883 | 0.05943 | 1.343e-27 | Study-level association; see design caveats |
| NCBI:GeneID:105322996 | nuclear protein AMMECR1 | log2 fold change | -4.032 | 0.3512 | 3.924e-27 | Study-level association; see design caveats |
| NCBI:GeneID:105345482 | BUB3-interacting and GLEBS motif-containing protein ZNF207 | log2 fold change | 0.4328 | 0.03853 | 5.978e-26 | Study-level association; see design caveats |
PRJNA1511593 — temperature
Study design, replication and limitations
No phenotype is deposited and no publication is linked; AREE records the gill transcriptional response to acute heat.
Not harmonized. Study-level descriptive work exists, but the design does not support the released inferential evidence table. See the study limitations.
PRJNA1511593 — temperature
Study design, replication and limitations
No phenotype is deposited and no publication is linked; AREE records the gill transcriptional response to acute heat.
Not harmonized. Study-level descriptive work exists, but the design does not support the released inferential evidence table. See the study limitations.
PRJNA407831 — temperature
Study design, replication and limitations
Intertidal-origin F1 oysters showed higher survival after acute heat stress (42 C, 1 h) and higher metabolic rates at 35 C than subtidal-origin oysters, with slower growth, and more transcriptional plasticity. AREE records the gill transcriptional response to 35 C averaged over the four populations, not survival per library.
Records: 23,666; genes with nonmissing raw p-values: 23,571. Study-level associations.
Adjusted p < 0.05: 935 (537 positive, 398 negative). Counts are study-level molecular associations.
Biological replication: 23 libraries analysed (24 sequenced; one 0 h outlier left out): 11 at 0 h and 12 at 6 h. Each library pools equal gill RNA from five oysters of one culture tank; four populations (two sites x intertidal or subtidal origin) x three tanks, and the same tanks are sampled at each time.
Treatment: Held in 35 C seawater (sublethal) for 6 h
Control: Same tanks sampled at 0 h, before the temperature was raised (laboratory acclimation 14.2-18.2 C)
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
Download all harmonized evidence
| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105348305 | heat shock protein 68-like | log2 fold change | 7.447 | 0.4301 | 9.028e-63 | Study-level association; see design caveats |
| NCBI:GeneID:105321326 | endoplasmic reticulum membrane sensor NFE2L1 | log2 fold change | -1.639 | 0.09711 | 8.064e-60 | Study-level association; see design caveats |
| NCBI:GeneID:105348304 | heat shock protein 68 | log2 fold change | 7.416 | 0.4469 | 6.047e-58 | Study-level association; see design caveats |
| NCBI:GeneID:117680673 | heat shock protein 68 | log2 fold change | 7.167 | 0.4555 | 5.242e-52 | Study-level association; see design caveats |
| NCBI:GeneID:136276074 | uncharacterized LOC136276074 | log2 fold change | -1.379 | 0.09153 | 1.297e-47 | Study-level association; see design caveats |
| NCBI:GeneID:105334510 | heat shock protein 68-like | log2 fold change | 7.167 | 0.4786 | 4.347e-47 | Study-level association; see design caveats |
| NCBI:GeneID:105334580 | BAG family molecular chaperone regulator 3 | log2 fold change | 5.375 | 0.3851 | 9.786e-41 | Study-level association; see design caveats |
| NCBI:GeneID:105348520 | UBA-like domain-containing protein 1 | log2 fold change | -0.4126 | 0.02985 | 5.426e-40 | Study-level association; see design caveats |
| NCBI:GeneID:105331566 | transcription factor MafK | log2 fold change | 0.6386 | 0.04924 | 4.813e-35 | Study-level association; see design caveats |
| NCBI:GeneID:105322996 | nuclear protein AMMECR1 | log2 fold change | -2.713 | 0.2226 | 8.974e-31 | Study-level association; see design caveats |
PRJEB86646 — temperature
Study design, replication and limitations
Lower mortality after OsHV-1 mu-Var cohabitation is favorable. The publication reports that 30 C limits POMS development and improves survival, through metabolic reprogramming and stronger baseline and induced antiviral immunity. AREE records the whole-spat transcriptional state at 30 C before infection, not survival per library.
Records: 25,395; genes with nonmissing raw p-values: 25,355. Study-level associations.
Adjusted p < 0.05: 9,024 (4,542 positive, 4,482 negative). Counts are study-level molecular associations.
Biological replication: 12 RNA-seq libraries, all sampled at 0 h post-cohabitation: 6 at 23 C and 6 at 30 C, three per temperature in each of the two families. Each library pools the soft tissue of 10 live spat taken from one tank, as in the DECICOMP starvation arm.
Treatment: Fed ad libitum and held at 30 C (non-permissive for POMS) through the DECICOMP acclimation (PRJEB86646)
Control: Fed ad libitum and held at 23 C (permissive for POMS) for 16 days (DECICOMP control arm, PRJEB86525)
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
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| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105327837 | uncharacterized LOC105327837 | log2 fold change | -3.836 | 0.1887 | 1.802e-87 | Study-level association; see design caveats |
| NCBI:GeneID:105345215 | uncharacterized LOC105345215 | log2 fold change | -5.755 | 0.3007 | 1.604e-77 | Study-level association; see design caveats |
| NCBI:GeneID:105337015 | uncharacterized LOC105337015 | log2 fold change | 1.416 | 0.08545 | 9.328e-58 | Study-level association; see design caveats |
| NCBI:GeneID:136273757 | heat shock protein beta-1-like | log2 fold change | 2.464 | 0.1656 | 2.939e-46 | Study-level association; see design caveats |
| NCBI:GeneID:105345603 | putative peptidyl-prolyl cis-trans isomerase | log2 fold change | -1.816 | 0.1227 | 7.559e-46 | Study-level association; see design caveats |
| NCBI:GeneID:117684197 | PE-PGRS family protein PE_PGRS47-like | log2 fold change | -3.805 | 0.2607 | 1.326e-44 | Study-level association; see design caveats |
| NCBI:GeneID:105323167 | small ribosomal subunit protein eS27-like | log2 fold change | 0.5764 | 0.03967 | 2.828e-44 | Study-level association; see design caveats |
| NCBI:GeneID:136272199 | uncharacterized LOC136272199 | log2 fold change | -2.52 | 0.1783 | 7.5e-42 | Study-level association; see design caveats |
| NCBI:GeneID:105329390 | asparagine synthetase [glutamine-hydrolyzing] | log2 fold change | -2.105 | 0.1508 | 8.075e-41 | Study-level association; see design caveats |
| NCBI:GeneID:136269995 | caspase-7-like | log2 fold change | 1.032 | 0.07784 | 1.074e-36 | Study-level association; see design caveats |
PRJNA516762 — temperature
Study design, replication and limitations
Organism-level thermal-tolerance direction was not measured; molecular heat-response direction only
Records: 22,397; genes with nonmissing raw p-values: 22,323. Study-level associations.
Adjusted p < 0.05: 99 (57 positive, 42 negative). Counts are study-level molecular associations.
Biological replication: Direct heat-versus-control contrast: 3 pooled RNA-seq libraries per condition, each pooling 5 individuals (30 individuals total; 6 libraries)
Treatment: 35 C seawater heat shock for 2 h without HSF1 RNAi
Control: Untreated control after 1 week acclimation at 12 +/- 1 C
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
Download all harmonized evidence
| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:117680673 | heat shock protein 68 | log2 fold change | 4.534 | 0.3459 | 5.341e-35 | Study-level association; see design caveats |
| NCBI:GeneID:105321326 | endoplasmic reticulum membrane sensor NFE2L1 | log2 fold change | -1.04 | 0.07957 | 5.341e-35 | Study-level association; see design caveats |
| NCBI:GeneID:105346578 | major egg antigen | log2 fold change | 4.158 | 0.3274 | 4.544e-33 | Study-level association; see design caveats |
| NCBI:GeneID:105317118 | uncharacterized LOC105317118 | log2 fold change | -1.493 | 0.1428 | 7.588e-22 | Study-level association; see design caveats |
| NCBI:GeneID:136271521 | uncharacterized LOC136271521 | log2 fold change | -4.935 | 0.492 | 4.919e-20 | Study-level association; see design caveats |
| NCBI:GeneID:105322484 | heat shock protein 68-like | log2 fold change | 5.327 | 0.5979 | 1.893e-15 | Study-level association; see design caveats |
| NCBI:GeneID:105321886 | uncharacterized LOC105321886 | log2 fold change | 1.986 | 0.2347 | 8.423e-14 | Study-level association; see design caveats |
| NCBI:GeneID:136271565 | uncharacterized LOC136271565 | log2 fold change | -3.382 | 0.4208 | 2.575e-12 | Study-level association; see design caveats |
| NCBI:GeneID:105334510 | heat shock protein 68-like | log2 fold change | 4.9 | 0.6138 | 3.552e-12 | Study-level association; see design caveats |
| NCBI:GeneID:105334814 | baculoviral IAP repeat-containing protein 2 | log2 fold change | 1.544 | 0.2027 | 5.847e-11 | Study-level association; see design caveats |
PRJNA593309 — temperature
Study design, replication and limitations
Survival 14 days after cohabitation was higher at 29 C (85.7%) than at 21 C (52.4%), and viral load rose more slowly at 29 C. AREE records the whole-oyster transcriptional difference at 12 h, not survival per library.
Records: 14,943; genes with nonmissing raw p-values: 14,937. Study-level associations.
Adjusted p < 0.05: 198 (30 positive, 168 negative). Counts are study-level molecular associations.
Biological replication: 5 oysters from 6 libraries: three at 21 C, each from a different tank, and two at 29 C, because two of the three 29 C libraries are the same oyster and were summed. The publication describes one oyster per tank, so the duplicated 29 C oyster means either one tank was sampled twice or one RNA was sequenced twice.
Treatment: Acclimated 10 days at 29 C (ramped 2 C per day from 21 C) and sampled 12 h after the start of OsHV-1 muVar cohabitation
Control: Acclimated at 21 C and sampled 12 h after the start of OsHV-1 muVar cohabitation
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
Download all harmonized evidence
| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105336969 | uncharacterized LOC105336969 | log2 fold change | -3.046 | 0.3322 | 6.716e-16 | Study-level association; see design caveats |
| NCBI:GeneID:105325126 | uncharacterized LOC105325126 | log2 fold change | -9.452 | 1.15 | 1.374e-12 | Study-level association; see design caveats |
| NCBI:GeneID:105318596 | NPC intracellular cholesterol transporter 2 | log2 fold change | -3.531 | 0.4371 | 2.979e-12 | Study-level association; see design caveats |
| NCBI:GeneID:105343649 | cerebellin-1 | log2 fold change | -5.048 | 0.6942 | 1.219e-09 | Study-level association; see design caveats |
| NCBI:GeneID:105327353 | natterin-4-like | log2 fold change | -3.658 | 0.5063 | 1.376e-09 | Study-level association; see design caveats |
| NCBI:GeneID:105340688 | NPC intracellular cholesterol transporter 2 | log2 fold change | -6.805 | 0.9786 | 8.175e-09 | Study-level association; see design caveats |
| NCBI:GeneID:117684150 | uncharacterized LOC117684150 | log2 fold change | -4.476 | 0.6472 | 9.129e-09 | Study-level association; see design caveats |
| NCBI:GeneID:117687426 | annexin A7-like | log2 fold change | -2.31 | 0.3417 | 2.397e-08 | Study-level association; see design caveats |
| NCBI:GeneID:105330356 | ETS-related transcription factor Elf-5 | log2 fold change | -3.098 | 0.4658 | 4.499e-08 | Study-level association; see design caveats |
| NCBI:GeneID:117680298 | uncharacterized LOC117680298 | log2 fold change | -4.104 | 0.6201 | 5.022e-08 | Study-level association; see design caveats |
PRJNA913164 — temperature
Study design, replication and limitations
Mortality was elevated in the stress treatments relative to the control. AREE records the ctenidium transcriptional response to elevated seawater temperature, not survival per library.
Records: 18,085; genes with nonmissing raw p-values: 18,085. Study-level associations.
Adjusted p < 0.05: 4,394 (2,216 positive, 2,178 negative). Counts are study-level molecular associations.
Biological replication: 44 ctenidium libraries analysed, one oyster each (23 controls and 21 treated after QC exclusions), from 48 sequenced: 24 controls and 24 30 C, 12 diploid and 12 triploid in each arm. The 24 control libraries are shared with CGIG_MULTISTRESS_RNASEQ_PRJNA913164 (30 C followed by 44 C emersion).
Treatment: Held submerged in 30 C seawater (single stressor, marine heatwave seawater temperature)
Control: Held submerged at 20 C (control)
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
Download all harmonized evidence
| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105329085 | high mobility group-T protein | log2 fold change | -2.213 | 0.08853 | 1.32e-133 | Study-level association; see design caveats |
| NCBI:GeneID:105342400 | serine/arginine-rich splicing factor 4 | log2 fold change | 1.683 | 0.07184 | 2.32e-117 | Study-level association; see design caveats |
| NCBI:GeneID:105341070 | DNA topoisomerase I, mitochondrial | log2 fold change | 1.459 | 0.06496 | 6.144e-108 | Study-level association; see design caveats |
| NCBI:GeneID:105336966 | calreticulin | log2 fold change | 1.892 | 0.08957 | 2.063e-95 | Study-level association; see design caveats |
| NCBI:GeneID:105323271 | zinc finger CCHC domain-containing protein 17 | log2 fold change | -1.547 | 0.08078 | 3.272e-78 | Study-level association; see design caveats |
| NCBI:GeneID:117680708 | serine/arginine-rich splicing factor 1 | log2 fold change | 1.786 | 0.09657 | 6.89e-73 | Study-level association; see design caveats |
| NCBI:GeneID:105344085 | nucleolin | log2 fold change | -2.043 | 0.1112 | 6.528e-72 | Study-level association; see design caveats |
| NCBI:GeneID:105347167 | heterogeneous nuclear ribonucleoprotein D-like | log2 fold change | -1.113 | 0.06962 | 3.515e-54 | Study-level association; see design caveats |
| NCBI:GeneID:105342698 | probable splicing factor, arginine/serine-rich 6 | log2 fold change | 1.424 | 0.08944 | 9.3e-54 | Study-level association; see design caveats |
| NCBI:GeneID:105341388 | protein disulfide-isomerase A6 | log2 fold change | 1.942 | 0.1247 | 2.099e-51 | Study-level association; see design caveats |
PRJNA298285 — temperature
Study design, replication and limitations
No phenotype is deposited and no publication is linked; AREE records the larval transcriptional response averaged over three developmental stages.
Not harmonized. Study-level descriptive work exists, but the design does not support the released inferential evidence table. See the study limitations.
PRJNA298285 — multi stressor exposure
Study design, replication and limitations
No phenotype is deposited and no publication is linked; AREE records the larval transcriptional response averaged over three developmental stages.
Not harmonized. Study-level descriptive work exists, but the design does not support the released inferential evidence table. See the study limitations.
PRJNA298285 — ocean acidification pH
Study design, replication and limitations
No phenotype is deposited and no publication is linked; AREE records the larval transcriptional response averaged over three developmental stages.
Records: 19,723; genes with nonmissing raw p-values: 19,723. Study-level associations.
Adjusted p < 0.05: 38 (25 positive, 13 negative). Counts are study-level molecular associations.
Biological replication: 12 whole-larva libraries: 6 ambient and 6 acidified (pH 7.9, 20 C), two per developmental stage. Each library is presumably a pool of many larvae; whether the two libraries per cell are separate cultures or one culture is not recorded and is tested with the expressed-SNP check.
Treatment: Reared at pH 7.9 and 20 C (acidified)
Control: Reared at pH 8.1 and 20 C (ambient)
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
Download all harmonized evidence
| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105342907 | uncharacterized LOC105342907 | log2 fold change | -0.7074 | 0.1109 | 3.516e-06 | Study-level association; see design caveats |
| NCBI:GeneID:136276238 | uncharacterized LOC136276238 | log2 fold change | 0.6331 | 0.1014 | 4.124e-06 | Study-level association; see design caveats |
| NCBI:GeneID:105319433 | uncharacterized LOC105319433 | log2 fold change | 0.6925 | 0.1182 | 2.893e-05 | Study-level association; see design caveats |
| NCBI:GeneID:105340265 | uncharacterized LOC105340265 | log2 fold change | 0.4336 | 0.07454 | 2.893e-05 | Study-level association; see design caveats |
| NCBI:GeneID:105336939 | early endosome antigen 1 | log2 fold change | 0.494 | 0.09384 | 0.0004702 | Study-level association; see design caveats |
| NCBI:GeneID:109620236 | uncharacterized LOC109620236 | log2 fold change | 0.3894 | 0.07405 | 0.0004702 | Study-level association; see design caveats |
| NCBI:GeneID:105331171 | uncharacterized LOC105331171 | log2 fold change | -1.152 | 0.2209 | 0.0005103 | Study-level association; see design caveats |
| NCBI:GeneID:105334837 | uncharacterized LOC105334837 | log2 fold change | 0.6711 | 0.1352 | 0.001671 | Study-level association; see design caveats |
| NCBI:GeneID:105331904 | uncharacterized LOC105331904 | log2 fold change | 0.359 | 0.07386 | 0.002521 | Study-level association; see design caveats |
| NCBI:GeneID:105318599 | uncharacterized LOC105318599 | log2 fold change | -0.9636 | 0.207 | 0.005306 | Study-level association; see design caveats |
PRJNA913164 — multi stressor exposure
Study design, replication and limitations
Mortality after the multiple stressor was higher in triploids than diploids (36.4% versus 14.8%), with metabolic depression and reduced ctenidium Na/K-ATPase activity in triploids. AREE records the ctenidium transcriptional response averaged over ploidy, not survival per library.
Records: 17,808; genes with nonmissing raw p-values: 17,808. Study-level associations.
Adjusted p < 0.05: 3,236 (1,655 positive, 1,581 negative). Counts are study-level molecular associations.
Biological replication: 42 ctenidium libraries analysed, one oyster each (23 controls and 19 treated after QC exclusions), from 48 sequenced: 24 controls and 24 30 C + 44 C emersion, 12 diploid and 12 triploid in each arm. The 24 control libraries are shared with CGIG_HEAT_RNASEQ_PRJNA913164 (30 C seawater only).
Treatment: Held in 30 C seawater, then emersed in air at 44 C for 6 h (multiple stressor, seawater heat followed by aerial heat over a tidal cycle)
Control: Held submerged at 20 C (control)
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
Download all harmonized evidence
| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105342400 | serine/arginine-rich splicing factor 4 | log2 fold change | 1.586 | 0.07232 | 2.431e-102 | Study-level association; see design caveats |
| NCBI:GeneID:105329085 | high mobility group-T protein | log2 fold change | -1.63 | 0.09076 | 3.775e-68 | Study-level association; see design caveats |
| NCBI:GeneID:105348423 | high mobility group box 1 | log2 fold change | -1.707 | 0.1012 | 5.11e-60 | Study-level association; see design caveats |
| NCBI:GeneID:105336966 | calreticulin | log2 fold change | 1.638 | 0.09784 | 2.962e-59 | Study-level association; see design caveats |
| NCBI:GeneID:117680708 | serine/arginine-rich splicing factor 1 | log2 fold change | 1.684 | 0.1071 | 3.494e-52 | Study-level association; see design caveats |
| NCBI:GeneID:105334510 | heat shock protein 68-like | log2 fold change | 8.484 | 0.588 | 1.008e-43 | Study-level association; see design caveats |
| NCBI:GeneID:117680673 | heat shock protein 68 | log2 fold change | 8.474 | 0.5898 | 2.12e-43 | Study-level association; see design caveats |
| NCBI:GeneID:105342698 | probable splicing factor, arginine/serine-rich 6 | log2 fold change | 1.469 | 0.1051 | 4.84e-41 | Study-level association; see design caveats |
| NCBI:GeneID:105348305 | heat shock protein 68-like | log2 fold change | 7.606 | 0.5463 | 8.902e-41 | Study-level association; see design caveats |
| NCBI:GeneID:105322484 | heat shock protein 68-like | log2 fold change | 5.518 | 0.3974 | 1.418e-40 | Study-level association; see design caveats |
PRJNA1196326 — ocean acidification pH
Study design, replication and limitations
The BioProject frames the study as transcriptional acclimation of offspring after parental acidification exposure; no larval performance or survival phenotype is deposited, so AREE records the larval transcriptional response to parental acidification, not a measured tolerance phenotype
Not harmonized. Study-level descriptive work exists, but the design does not support the released inferential evidence table. See the study limitations.
PRJNA735889 — ocean acidification pH
Study design, replication and limitations
Lutier et al. report physiological tipping points at pHT 7.3-6.9 that coincide with a major reshuffling of the transcriptome and membrane lipids; AREE records the whole-animal transcriptional response below the tipping window relative to above it, not a measured tolerance phenotype
Records: 28,811; genes with nonmissing raw p-values: 28,811. Exploratory; nominal FDR not used.
Exploratory: Tank clustering is unmodeled. Nominal significance and uncertainty may overstate precision; descriptive findings are shown without inferential claims.
Biological replication: 50 oysters, one whole-animal library each: 25 control and 25 acidified, 5 per tank. A 51st library, 13Ebis, is a resequencing of oyster 13E and is not analysed. Each pH level is one tank, so oysters are replicates within tank and the 10 tanks are the replicates of the pH contrast.
Treatment: Juveniles held 23 days at mean pHT 6.5-6.8 (tanks 9 and 15 at 6.5, 16 at 6.6, 7 at 6.7, 14 at 6.8), below the 7.3-6.9 tipping-point window the authors report; condition label acidified
Control: Juveniles held 23 days at mean pHT 7.4-7.8 (tanks 13 at 7.4, 17 at 7.5, 8 at 7.6, 5 at 7.7, 3 at 7.8), above the tipping-point window; condition label control. No tank was held at ambient pH (about 8.0).
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
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| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105321906 | uncharacterized LOC105321906 | log2 fold change | 9.398 | 3.201 | 0.02568 (nominal only) | Exploratory; tank clustering unmodeled |
| NCBI:GeneID:105321243 | uncharacterized LOC105321243 | log2 fold change | 9.064 | 0.9061 | 1.041e-19 (nominal only) | Exploratory; tank clustering unmodeled |
| NCBI:GeneID:136271332 | uncharacterized protein MAL13P1.336-like | log2 fold change | 7.354 | 2.628 | 0.03516 (nominal only) | Exploratory; tank clustering unmodeled |
| NCBI:GeneID:136275927 | uncharacterized LOC136275927 | log2 fold change | -6.765 | 1.037 | 2.427e-08 (nominal only) | Exploratory; tank clustering unmodeled |
| NCBI:GeneID:136273810 | N66 matrix protein-like | log2 fold change | -6.685 | 0.9211 | 2.724e-10 (nominal only) | Exploratory; tank clustering unmodeled |
| NCBI:GeneID:105332517 | BPTI/Kunitz domain-containing protein-like | log2 fold change | 6.534 | 0.6686 | 8.398e-19 (nominal only) | Exploratory; tank clustering unmodeled |
| NCBI:GeneID:136275342 | natterin-4-like | log2 fold change | -6.464 | 3.193 | 0.1569 (nominal only) | Exploratory; tank clustering unmodeled |
| NCBI:GeneID:117683496 | uncharacterized LOC117683496 | log2 fold change | 6.339 | 0.6678 | 1.062e-17 (nominal only) | Exploratory; tank clustering unmodeled |
| NCBI:GeneID:136272817 | histone H3 | log2 fold change | -5.969 | 1.675 | 0.005062 (nominal only) | Exploratory; tank clustering unmodeled |
| NCBI:GeneID:136273936 | uncharacterized LOC136273936 | log2 fold change | 5.719 | 2.675 | 0.1292 (nominal only) | Exploratory; tank clustering unmodeled |
PRJNA826964 — ocean acidification pH
Study design, replication and limitations
The BioProject title frames acidification as compromising energy management; AREE records the hepatopancreas transcriptional response to acidification, not a measured organism-level energetic or survival phenotype
Records: 24,681; genes with nonmissing raw p-values: 24,681. Study-level associations.
Adjusted p < 0.05: 890 (301 positive, 589 negative). Counts are study-level molecular associations.
Biological replication: 6 pooled RNA samples, one per arm at each of 7, 28 and 56 days, each sequenced as three libraries (18 libraries); the BioSample records call the libraries biological replicates, but their genotypes show each set of three is one pool of several oysters
Treatment: Laboratory ocean acidification exposure sampled after 7, 28 and 56 days
Control: Ambient-seawater controls sampled at the same three time points
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
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| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105346234 | uncharacterized LOC105346234 | log2 fold change | -2.353 | 0.1739 | 2.558e-37 | Study-level association; see design caveats |
| NCBI:GeneID:105332163 | equilibrative nucleobase transporter 1 | log2 fold change | -3.767 | 0.3187 | 3.787e-28 | Study-level association; see design caveats |
| NCBI:GeneID:105326186 | uncharacterized LOC105326186 | log2 fold change | 1.845 | 0.1603 | 9.658e-27 | Study-level association; see design caveats |
| NCBI:GeneID:117686226 | uncharacterized LOC117686226 | log2 fold change | -5.686 | 0.5064 | 1.795e-25 | Study-level association; see design caveats |
| NCBI:GeneID:105342677 | ATP-dependent DNA helicase RecQ | log2 fold change | -3.568 | 0.3218 | 6.979e-25 | Study-level association; see design caveats |
| NCBI:GeneID:136273029 | tigger transposable element-derived protein 4-like | log2 fold change | -4.655 | 0.4222 | 1.181e-24 | Study-level association; see design caveats |
| NCBI:GeneID:105345639 | tigger transposable element-derived protein 4 | log2 fold change | -4.593 | 0.4191 | 2.037e-24 | Study-level association; see design caveats |
| NCBI:GeneID:105333978 | uncharacterized LOC105333978 | log2 fold change | 2.096 | 0.1958 | 2.793e-23 | Study-level association; see design caveats |
| NCBI:GeneID:117687150 | uncharacterized LOC117687150 | log2 fold change | 6.369 | 0.6416 | 8.594e-20 | Study-level association; see design caveats |
| NCBI:GeneID:117691483 | perlucin-like | log2 fold change | -1.52 | 0.156 | 5.013e-19 | Study-level association; see design caveats |
PRJNA1329250 — pathogen challenge
Study design, replication and limitations
Infection up-regulated antiviral defense transcripts, including RIG-I-like receptors and the interferon-like pathway, similarly in both lineages; AREE records molecular antiviral responsiveness, not an organism-level survival difference
Records: 27,917; genes with nonmissing raw p-values: 27,890. Study-level associations.
Adjusted p < 0.05: 5,446 (3,237 positive, 2,209 negative). Counts are study-level molecular associations.
Biological replication: 42 RNA-seq libraries: 12 controls (6 Midori, 6 Miyagi) and 30 OsHV-1 microvariant-challenged (15 Midori, 15 Miyagi, split across USA, Australia, and France viral strains at 5 libraries per lineage-strain cell)
Treatment: Experimental challenge with OsHV-1 microvariant (USA, Australia, or France strain)
Control: Unchallenged control spat from the same two lineages
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
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| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:136276189 | NFX1-type zinc finger-containing protein 1-like | log2 fold change | 2.336 | 0.1913 | 6.714e-30 | Study-level association; see design caveats |
| NCBI:GeneID:105343525 | myb-like protein X | log2 fold change | 3.161 | 0.2669 | 1.93e-28 | Study-level association; see design caveats |
| NCBI:GeneID:117689278 | uncharacterized LOC117689278 | log2 fold change | 2.911 | 0.2456 | 1.93e-28 | Study-level association; see design caveats |
| NCBI:GeneID:105336469 | NFX1-type zinc finger-containing protein 1 | log2 fold change | 2.547 | 0.2279 | 3.407e-25 | Study-level association; see design caveats |
| NCBI:GeneID:136276198 | uncharacterized LOC136276198 | log2 fold change | 2.477 | 0.2239 | 9.957e-25 | Study-level association; see design caveats |
| NCBI:GeneID:136269423 | uncharacterized LOC136269423 | log2 fold change | 3.067 | 0.2909 | 2.326e-22 | Study-level association; see design caveats |
| NCBI:GeneID:109617603 | uncharacterized LOC109617603 | log2 fold change | 2.425 | 0.2367 | 4.624e-21 | Study-level association; see design caveats |
| NCBI:GeneID:105345480 | probable ATP-dependent RNA helicase DDX46 | log2 fold change | 3.101 | 0.3058 | 1.177e-20 | Study-level association; see design caveats |
| NCBI:GeneID:136270275 | 3’-5’ exoribonuclease HELZ2-like | log2 fold change | 2.854 | 0.2847 | 3.48e-20 | Study-level association; see design caveats |
| NCBI:GeneID:109618139 | sacsin | log2 fold change | 2.319 | 0.2344 | 1.139e-19 | Study-level association; see design caveats |
PRJNA593309 — pathogen challenge
Study design, replication and limitations
At 21 C survival 14 days after cohabitation was 52.4%, and OsHV-1 DNA had reached high levels in all three oysters sampled at 48 h. AREE records the whole-oyster transcriptional response to infection, not survival per library.
Records: 14,555; genes with nonmissing raw p-values: 14,520. Study-level associations.
Adjusted p < 0.05: 846 (663 positive, 183 negative). Counts are study-level molecular associations.
Biological replication: 6 libraries, one whole 8-month-old oyster per tank: three at 0 h and three at 48 h, the same three 21 C tanks sampled at both times.
Treatment: 48 h after the start of cohabitation with OsHV-1 muVar-injected donor oysters at 21 C
Control: Same 21 C tanks sampled at 0 h, when donors were added (uninfected baseline)
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
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| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105343805 | interferon regulatory factor 2 | log2 fold change | 4.932 | 0.3748 | 2.179e-35 | Study-level association; see design caveats |
| NCBI:GeneID:105345480 | probable ATP-dependent RNA helicase DDX46 | log2 fold change | 4.996 | 0.4208 | 1.203e-28 | Study-level association; see design caveats |
| NCBI:GeneID:105325188 | DNA polymerase III PolC-type-like | log2 fold change | 8.662 | 0.7737 | 2.077e-25 | Study-level association; see design caveats |
| NCBI:GeneID:105334815 | baculoviral IAP repeat-containing protein 2 | log2 fold change | 6.415 | 0.586 | 2.453e-24 | Study-level association; see design caveats |
| NCBI:GeneID:105342241 | hypothetical protein | log2 fold change | 8.349 | 0.7757 | 1.492e-23 | Study-level association; see design caveats |
| NCBI:GeneID:105331509 | uncharacterized LOC105331509 | log2 fold change | 6.963 | 0.6645 | 2.601e-22 | Study-level association; see design caveats |
| NCBI:GeneID:117689263 | uncharacterized LOC117689263 | log2 fold change | 4.29 | 0.4146 | 8.926e-22 | Study-level association; see design caveats |
| NCBI:GeneID:105319712 | interferon-induced helicase C domain-containing protein 1 | log2 fold change | 4.815 | 0.4692 | 1.877e-21 | Study-level association; see design caveats |
| NCBI:GeneID:105332871 | uncharacterized LOC105332871 | log2 fold change | 13.99 | 1.39 | 1.279e-20 | Study-level association; see design caveats |
| NCBI:GeneID:105325524 | uncharacterized LOC105325524 | log2 fold change | 6.538 | 0.6582 | 4.279e-20 | Study-level association; see design caveats |
PRJEB58194 — pollutant exposure
Study design, replication and limitations
The publication found no difference in embryo-larval abnormalities at 24 hpf, disturbed swimming, larger and heavier exposed larvae at some times, a lower epinephrine-induced metamorphosis rate and higher field survival, and differential expression of developmental genes (Hox orthologues, cell-cycle regulators) in gastrulae. AREE records the transcriptional response averaged over two stages.
Records: 21,104; genes with nonmissing raw p-values: 21,104. Study-level associations.
Adjusted p < 0.05: 644 (255 positive, 389 negative). Counts are study-level molecular associations.
Biological replication: 36 libraries: 18 control and 18 exposed, nine per stage (gastrula, D larva), labelled with group digits 1-3 and replicate letters A-F.
Treatment: Exposed to the pesticide mixture from 0 to 48 h post fertilization; sampled as gastrulae (6 hpf) and D larvae
Control: Unexposed F0 gastrulae and D larvae from the same hatchery cohort
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
Download all harmonized evidence
| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:136270632 | cytochrome P450 2C14-like | log2 fold change | -2.337 | 0.3495 | 3.396e-07 | Study-level association; see design caveats |
| NCBI:GeneID:117684588 | forkhead box protein J3 | log2 fold change | 1.42 | 0.2143 | 3.396e-07 | Study-level association; see design caveats |
| NCBI:GeneID:105318673 | hypothetical protein | log2 fold change | -1.728 | 0.2652 | 4.683e-07 | Study-level association; see design caveats |
| NCBI:GeneID:105344432 | M-phase inducer phosphatase | log2 fold change | 1.898 | 0.3138 | 7.107e-06 | Study-level association; see design caveats |
| NCBI:GeneID:136270694 | eggshell protein-like | log2 fold change | -2.098 | 0.3616 | 2.534e-05 | Study-level association; see design caveats |
| NCBI:GeneID:117683535 | uncharacterized LOC117683535 | log2 fold change | -2.448 | 0.4302 | 4.093e-05 | Study-level association; see design caveats |
| NCBI:GeneID:105318858 | homeobox protein engrailed-1-B | log2 fold change | -1.405 | 0.2486 | 4.403e-05 | Study-level association; see design caveats |
| NCBI:GeneID:105319984 | low-density lipoprotein receptor-related protein 12 | log2 fold change | -1.609 | 0.2898 | 5.838e-05 | Study-level association; see design caveats |
| NCBI:GeneID:105338625 | fatty acid 2-hydroxylase | log2 fold change | -1.169 | 0.2109 | 5.838e-05 | Study-level association; see design caveats |
| NCBI:GeneID:105345534 | uncharacterized LOC105345534 | log2 fold change | -0.8291 | 0.1489 | 5.838e-05 | Study-level association; see design caveats |
PRJEB58194 — pollutant exposure
Study design, replication and limitations
The publication found that the parents’ exposure shaped the offspring phenotype more than direct exposure did; offspring of exposed parents had lower epinephrine-induced metamorphosis and field survival. AREE records the transcriptional response to direct exposure averaged over two stages.
Records: 24,306; genes with nonmissing raw p-values: 24,285. Study-level associations.
Adjusted p < 0.05: 17 (1 positive, 16 negative). Counts are study-level molecular associations.
Biological replication: 12 libraries: 6 TT and 6 TE, three per stage.
Treatment: F1 offspring of control parents exposed to the pesticide mixture from 0 to 48 h post fertilization (TE); sampled as gastrulae (6 hpf) and metamorphosis-competent pediveligers
Control: F1 offspring of control parents, unexposed (TT)
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
Download all harmonized evidence
| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105321667 | uncharacterized LOC105321667 | log2 fold change | -3.722 | 0.528 | 4.331e-08 | Study-level association; see design caveats |
| NCBI:GeneID:105345214 | uncharacterized LOC105345214 | log2 fold change | -2.051 | 0.3173 | 1.243e-06 | Study-level association; see design caveats |
| NCBI:GeneID:136275506 | uncharacterized LOC136275506 | log2 fold change | -2.441 | 0.4173 | 3.962e-05 | Study-level association; see design caveats |
| NCBI:GeneID:105344419 | protein GrpE | log2 fold change | -2.076 | 0.3704 | 0.000127 | Study-level association; see design caveats |
| NCBI:GeneID:105330869 | uncharacterized LOC105330869 | log2 fold change | -1.551 | 0.2941 | 0.0006439 | Study-level association; see design caveats |
| NCBI:GeneID:117684421 | protein starmaker | log2 fold change | -1.61 | 0.3196 | 0.001925 | Study-level association; see design caveats |
| NCBI:GeneID:105339864 | WAG22 antigen | log2 fold change | -2.992 | 0.614 | 0.003812 | Study-level association; see design caveats |
| NCBI:GeneID:117689738 | glycine-rich protein 1 | log2 fold change | -2.316 | 0.4806 | 0.004386 | Study-level association; see design caveats |
| NCBI:GeneID:105325539 | caveolin-3-like | log2 fold change | -3.195 | 0.7068 | 0.01671 | Study-level association; see design caveats |
| NCBI:GeneID:105330462 | shematrin-like protein 2 | log2 fold change | -3.629 | 0.8185 | 0.02044 | Study-level association; see design caveats |
PRJEB58194 — pollutant exposure
Study design, replication and limitations
The publication found that parental exposure drove the offspring phenotype more than direct exposure: offspring of exposed parents had lower epinephrine-induced metamorphosis and field survival, and RNA-seq and methyl-seq separated offspring by F0 treatment. AREE records the intergenerational transcriptional effect averaged over two stages.
Not harmonized. Study-level descriptive work exists, but the design does not support the released inferential evidence table. See the study limitations.
PRJNA756710 — salinity
Study design, replication and limitations
Higher mortality after Vibrio infection is unfavorable; infected oysters reached 100% mortality at 10 ppt versus 33% at 30 ppt over 12 days (log-rank p < 0.01, n = 30 per tank in triplicate). AREE records the gill transcriptional response to low salinity during infection, not survival per library.
Records: 21,486; genes with nonmissing raw p-values: 21,098. Study-level associations.
Adjusted p < 0.05: 3,045 (1,825 positive, 1,220 negative). Counts are study-level molecular associations.
Biological replication: 12 RNA-seq libraries used for the contrast: 6 at 30 ppt and 6 at 10 ppt, three per salinity at each of 12 h and 48 h. Each library pools equal gill tissue from three oysters taken from one tank. Two further 0 h libraries (SRR15559848, SRR15559847) are shared pre-transfer baselines with no salinity contrast and are not used.
Treatment: Intramuscular injection of Vibrio alginolyticus (50 uL of 5 x 10^8 CFU/mL) followed by transfer to 10 ppt seawater (“10‰Vibrio”)
Control: The same Vibrio alginolyticus injection followed by holding at the 30 ppt acclimation salinity (“30‰Vibrio”)
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
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| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105321584 | cysteine sulfinic acid decarboxylase | log2 fold change | 8.529 | 0.4266 | 1.303e-84 | Study-level association; see design caveats |
| NCBI:GeneID:105334814 | baculoviral IAP repeat-containing protein 2 | log2 fold change | 4.683 | 0.3063 | 9.378e-49 | Study-level association; see design caveats |
| NCBI:GeneID:105317679 | carnosine synthase 1 | log2 fold change | 7.595 | 0.5116 | 5.365e-46 | Study-level association; see design caveats |
| NCBI:GeneID:105335765 | uncharacterized LOC105335765 | log2 fold change | 6.519 | 0.4929 | 3.327e-36 | Study-level association; see design caveats |
| NCBI:GeneID:105329513 | dual specificity protein phosphatase 10 | log2 fold change | 3.14 | 0.238 | 4.159e-36 | Study-level association; see design caveats |
| NCBI:GeneID:105321886 | uncharacterized LOC105321886 | log2 fold change | 5.556 | 0.4359 | 1.141e-33 | Study-level association; see design caveats |
| NCBI:GeneID:105340455 | uncharacterized LOC105340455 | log2 fold change | 7.113 | 0.5712 | 4.09e-32 | Study-level association; see design caveats |
| NCBI:GeneID:105325560 | class E basic helix-loop-helix protein 40 | log2 fold change | 2.255 | 0.2153 | 3.047e-22 | Study-level association; see design caveats |
| NCBI:GeneID:136273671 | uncharacterized LOC136273671 | log2 fold change | 4.23 | 0.4051 | 3.737e-22 | Study-level association; see design caveats |
| NCBI:GeneID:105324933 | platelet-activating factor acetylhydrolase | log2 fold change | 3.503 | 0.345 | 6.569e-21 | Study-level association; see design caveats |
PRJEB86618 — nutritional limitation
Study design, replication and limitations
Lower mortality after OsHV-1 mu-Var cohabitation is favorable. Starved spat had lower final mortality than fed spat (F14R 34.8% versus 75.5%; F11N 93.3% versus 100%; log-rank p < 0.05 in both families), and deaths began later (120 h versus 72-96 h post-cohabitation). AREE records the whole-spat transcriptional state produced by starvation before infection, not survival per library.
Records: 25,301; genes with nonmissing raw p-values: 25,253. Study-level associations.
Adjusted p < 0.05: 11,930 (5,941 positive, 5,989 negative). Counts are study-level molecular associations.
Biological replication: 12 RNA-seq libraries used for the contrast, all sampled at 0 h post-cohabitation: 6 fed and 6 starved, three per diet in each of the two families. Each library pools the soft tissue of 10 live spat taken from one tank. The experiment used three tanks per diet, and each tank held both families.
Treatment: Starved for 16 days at 23 C (DECICOMP nutritional-stress arm, PRJEB86618)
Control: Fed phytoplankton ad libitum for 16 days at 23 C (DECICOMP control arm, PRJEB86525)
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
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| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105327731 | serine protease inhibitor Cvsi-1 | log2 fold change | -3.317 | 0.1321 | 1.008e-134 | Study-level association; see design caveats |
| NCBI:GeneID:105318596 | NPC intracellular cholesterol transporter 2 | log2 fold change | -3.78 | 0.1552 | 6.468e-127 | Study-level association; see design caveats |
| NCBI:GeneID:105328194 | uncharacterized LOC105328194 | log2 fold change | -2.744 | 0.1129 | 1.668e-126 | Study-level association; see design caveats |
| NCBI:GeneID:105318146 | uncharacterized LOC105318146 | log2 fold change | -3.824 | 0.159 | 4.43e-124 | Study-level association; see design caveats |
| NCBI:GeneID:105317784 | serine protease 33 | log2 fold change | -2.592 | 0.1102 | 1.091e-118 | Study-level association; see design caveats |
| NCBI:GeneID:136269432 | lectin BRA-3-like | log2 fold change | -2.7 | 0.1187 | 8.138e-111 | Study-level association; see design caveats |
| NCBI:GeneID:105346974 | L-sorbose 1-dehydrogenase | log2 fold change | -3.072 | 0.1392 | 2.335e-104 | Study-level association; see design caveats |
| NCBI:GeneID:105334885 | patched domain-containing protein 3 | log2 fold change | -3.36 | 0.1566 | 1.429e-98 | Study-level association; see design caveats |
| NCBI:GeneID:105330227 | isocitrate dehydrogenase [NADP] cytoplasmic | log2 fold change | -1.519 | 0.07174 | 4.425e-96 | Study-level association; see design caveats |
| NCBI:GeneID:105348230 | uncharacterized LOC105348230 | log2 fold change | -2.066 | 0.1018 | 3.782e-88 | Study-level association; see design caveats |
PRJNA694496 — temperature
Study design, replication and limitations
Selected population had higher post-heat-shock survival (78.05% versus 66.34%) and field summer survival (73% versus 62%)
Records: 19,816; genes with nonmissing raw p-values: 19,814. Study-level associations.
Adjusted p < 0.05: 8,802 (4,353 positive, 4,449 negative). Counts are study-level molecular associations.
Biological replication: RNA-seq: 3 selected-population and 3 control-population larval libraries; number of larvae pooled per library was not reported
Treatment: F2 population after two generations of artificial selection using 42 C heat shock for 1 h; larvae sampled at ambient hatchery conditions
Control: F2 non-selected control population; larvae sampled at ambient hatchery conditions
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
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| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:117686572 | sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1 | log2 fold change | -5.921 | 0.1873 | 4.562e-215 | Study-level association; see design caveats |
| NCBI:GeneID:105331877 | uncharacterized LOC105331877 | log2 fold change | -4.373 | 0.1681 | 3.255e-145 | Study-level association; see design caveats |
| NCBI:GeneID:105338552 | uncharacterized LOC105338552 | log2 fold change | -3.126 | 0.1263 | 2.561e-131 | Study-level association; see design caveats |
| NCBI:GeneID:117681484 | transforming growth factor-beta-induced protein ig-h3-like | log2 fold change | -4.293 | 0.1912 | 5.482e-108 | Study-level association; see design caveats |
| NCBI:GeneID:105318991 | sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1 | log2 fold change | -3.391 | 0.1591 | 3.303e-97 | Study-level association; see design caveats |
| NCBI:GeneID:105321245 | uncharacterized LOC105321245 | log2 fold change | -3.991 | 0.1896 | 7.208e-95 | Study-level association; see design caveats |
| NCBI:GeneID:117686571 | sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1 | log2 fold change | -4.95 | 0.2363 | 5.486e-94 | Study-level association; see design caveats |
| NCBI:GeneID:105340999 | A disintegrin and metalloproteinase with thrombospondin motifs adt-1 | log2 fold change | 5.905 | 0.2876 | 2.603e-90 | Study-level association; see design caveats |
| NCBI:GeneID:105323084 | SCO-spondin | log2 fold change | -3.003 | 0.15 | 7.632e-86 | Study-level association; see design caveats |
| NCBI:GeneID:105344090 | mesenchyme-specific cell surface glycoprotein | log2 fold change | -4.965 | 0.2537 | 4.474e-82 | Study-level association; see design caveats |
PRJNA856813 — pollutant exposure
Study design, replication and limitations
The publication reports activation of energy metabolism and stress responses under leachate exposure, signs of microbiota dysbiosis at high concentrations, reduced sperm motility and oocyte transcriptional changes, but no significant ecophysiological change in adults and no effect on offspring growth, which it interprets as possible resilience. AREE records the gill transcriptional response, not a measured phenotype per library.
Records: 15,278; genes with nonmissing raw p-values: 15,150. Study-level associations.
Adjusted p < 0.05: 46 (26 positive, 20 negative). Counts are study-level molecular associations.
Biological replication: 12 day-41 gill libraries, one oyster each: 6 controls and 6 high-concentration leachate oysters.
Treatment: Exposed for 41 days to the high concentration of tire leachate (chemicals released from tire particles, without the particles)
Control: Unexposed control oysters, gill sampled on day 41
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
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| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105341503 | double-stranded RNA-specific adenosine deaminase | log2 fold change | 4.413 | 0.7364 | 1.559e-05 | Study-level association; see design caveats |
| NCBI:GeneID:136270275 | 3’-5’ exoribonuclease HELZ2-like | log2 fold change | 3.544 | 0.5906 | 1.559e-05 | Study-level association; see design caveats |
| NCBI:GeneID:136273219 | uncharacterized LOC136273219 | log2 fold change | 7.501 | 1.283 | 2.567e-05 | Study-level association; see design caveats |
| NCBI:GeneID:136271462 | protein unc-13 homolog C-like | log2 fold change | 5.403 | 1.02 | 0.0004473 | Study-level association; see design caveats |
| NCBI:GeneID:105347083 | small nuclear ribonucleoprotein E | log2 fold change | -1.492 | 0.2875 | 0.0006375 | Study-level association; see design caveats |
| NCBI:GeneID:136270277 | uncharacterized LOC136270277 | log2 fold change | 4.32 | 0.8722 | 0.001848 | Study-level association; see design caveats |
| NCBI:GeneID:117686169 | uncharacterized LOC117686169 | log2 fold change | -2.183 | 0.4486 | 0.002454 | Study-level association; see design caveats |
| NCBI:GeneID:105344283 | agmatinase, mitochondrial | log2 fold change | 2.087 | 0.4459 | 0.004293 | Study-level association; see design caveats |
| NCBI:GeneID:117686837 | transient receptor potential cation channel subfamily M member-like 2 | log2 fold change | 1.805 | 0.387 | 0.004293 | Study-level association; see design caveats |
| NCBI:GeneID:105346129 | acyl-CoA desaturase | log2 fold change | 1.359 | 0.2916 | 0.004293 | Study-level association; see design caveats |
PRJNA856813 — pollutant exposure
Study design, replication and limitations
The publication reports activation of energy metabolism and stress responses under leachate exposure, signs of microbiota dysbiosis at high concentrations, reduced sperm motility and oocyte transcriptional changes, but no significant ecophysiological change in adults and no effect on offspring growth, which it interprets as possible resilience. AREE records the gill transcriptional response, not a measured phenotype per library.
Records: 15,141; genes with nonmissing raw p-values: 15,081. Study-level associations.
Adjusted p < 0.05: 8 (5 positive, 3 negative). Counts are study-level molecular associations.
Biological replication: 12 day-41 gill libraries, one oyster each: 6 controls and 6 high-concentration tire-particle oysters.
Treatment: Exposed for 41 days to the high concentration of tire microparticles
Control: Unexposed control oysters, gill sampled on day 41
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
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| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:136276270 | ankyrin-1-like | log2 fold change | 4.438 | 0.7574 | 7.037e-05 | Study-level association; see design caveats |
| NCBI:GeneID:136276553 | uncharacterized LOC136276553 | log2 fold change | -5.893 | 1.127 | 0.0008624 | Study-level association; see design caveats |
| NCBI:GeneID:136271533 | uncharacterized LOC136271533 | log2 fold change | 4.826 | 0.9196 | 0.0008624 | Study-level association; see design caveats |
| NCBI:GeneID:105346492 | uncharacterized LOC105346492 | log2 fold change | 0.8478 | 0.1663 | 0.001292 | Study-level association; see design caveats |
| NCBI:GeneID:109617704 | uncharacterized LOC109617704 | log2 fold change | 4.706 | 1.082 | 0.02578 | Study-level association; see design caveats |
| NCBI:GeneID:117687253 | scavenger receptor class F member 1-like | log2 fold change | -2.787 | 0.6355 | 0.02578 | Study-level association; see design caveats |
| NCBI:GeneID:105332528 | baculoviral IAP repeat-containing protein 8 | log2 fold change | 2.251 | 0.5147 | 0.02578 | Study-level association; see design caveats |
| NCBI:GeneID:105320455 | protein mono-ADP-ribosyltransferase PARP6 | log2 fold change | -1.34 | 0.3033 | 0.02578 | Study-level association; see design caveats |
PRJNA515169 — pathogen challenge
Study design, replication and limitations
Virulent V. crassostreae J2-9 killed about 60% of oysters within 3 days, through contact-dependent hemocyte lysis requiring the r5.7 gene. AREE records the 8 h whole-spat transcriptional response to infection, not survival per library.
Records: 24,134; genes with nonmissing raw p-values: 24,134. Study-level associations.
Adjusted p < 0.05: 559 (453 positive, 106 negative). Counts are study-level molecular associations.
Biological replication: 6 libraries, each a pool of 30 spat: one mock and one V. crassostreae J2-9 pool from each of three independent infection experiments. Pools of 30 animals average out individual variation, so replication is at the level of experiments.
Treatment: Injected into the adductor muscle with 7.5 x 10^7 CFU of the virulent Vibrio crassostreae J2-9 and sampled 8 h later
Control: Mock-injected with sterile seawater and sampled 8 h later (sample alias ‘anesthesis’)
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
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| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105321376 | EF-hand calcium-binding domain-containing protein 1 | log2 fold change | 3.498 | 0.1361 | 2.734e-141 | Study-level association; see design caveats |
| NCBI:GeneID:136273704 | coadhesin-like | log2 fold change | 3.251 | 0.1567 | 1.285e-91 | Study-level association; see design caveats |
| NCBI:GeneID:136270488 | uncharacterized LOC136270488 | log2 fold change | 3.542 | 0.1894 | 3.114e-74 | Study-level association; see design caveats |
| NCBI:GeneID:136273062 | galanin receptor 2b-like | log2 fold change | 2.33 | 0.1377 | 1.605e-60 | Study-level association; see design caveats |
| NCBI:GeneID:105342241 | hypothetical protein | log2 fold change | 4.643 | 0.2928 | 5.234e-53 | Study-level association; see design caveats |
| NCBI:GeneID:105318026 | tumor necrosis factor receptor superfamily member 11A | log2 fold change | 2.932 | 0.1858 | 1.448e-52 | Study-level association; see design caveats |
| NCBI:GeneID:136276560 | uncharacterized LOC136276560 | log2 fold change | 3.787 | 0.2664 | 2.16e-42 | Study-level association; see design caveats |
| NCBI:GeneID:105322542 | interleukin 17-like protein | log2 fold change | 3.942 | 0.2819 | 4.993e-41 | Study-level association; see design caveats |
| NCBI:GeneID:105321692 | cytochrome P450 2C31-like | log2 fold change | 2.469 | 0.1795 | 1.071e-39 | Study-level association; see design caveats |
| NCBI:GeneID:105320131 | prostaglandin E2 receptor EP4 subtype | log2 fold change | 2.409 | 0.1768 | 6.175e-39 | Study-level association; see design caveats |
PRJNA852380 — pathogen challenge
Study design, replication and limitations
No phenotype is deposited; AREE records the digestive-gland transcriptional response to Vibrio exposure.
Records: 20,757; genes with nonmissing raw p-values: 20,718. Study-level associations.
Adjusted p < 0.05: 1,233 (859 positive, 374 negative). Counts are study-level molecular associations.
Biological replication: 6 digestive-gland libraries: 3 controls and 3 at 12 h after Vibrio exposure. Each library is a pool by expressed-SNP genotype; pool size is not recorded.
Treatment: Exposed to Vibrio and sampled 12 h later (species, dose and route not stated in the metadata)
Control: Unexposed control oysters
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
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| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105318026 | tumor necrosis factor receptor superfamily member 11A | log2 fold change | 4.3 | 0.3213 | 1.148e-36 | Study-level association; see design caveats |
| NCBI:GeneID:105320719 | melatonin receptor type 1A-like | log2 fold change | 1.867 | 0.1563 | 5.262e-29 | Study-level association; see design caveats |
| NCBI:GeneID:105347306 | myeloid differentiation primary response protein MyD88-like | log2 fold change | 3.844 | 0.3302 | 1.245e-27 | Study-level association; see design caveats |
| NCBI:GeneID:105321257 | proline-rich transmembrane protein 1 | log2 fold change | 5.857 | 0.5062 | 2.173e-27 | Study-level association; see design caveats |
| NCBI:GeneID:105329265 | L-threonine 3-dehydrogenase, mitochondrial | log2 fold change | 2.633 | 0.2358 | 1.821e-25 | Study-level association; see design caveats |
| NCBI:GeneID:105320131 | prostaglandin E2 receptor EP4 subtype | log2 fold change | 2.2 | 0.1999 | 9.131e-25 | Study-level association; see design caveats |
| NCBI:GeneID:105321692 | cytochrome P450 2C31-like | log2 fold change | 2.362 | 0.2211 | 2.636e-23 | Study-level association; see design caveats |
| NCBI:GeneID:136276180 | uncharacterized LOC136276180 | log2 fold change | 2.474 | 0.2344 | 9.166e-23 | Study-level association; see design caveats |
| NCBI:GeneID:105323667 | metalloproteinase inhibitor 2-like | log2 fold change | 1.712 | 0.1629 | 1.269e-22 | Study-level association; see design caveats |
| NCBI:GeneID:105342835 | cAMP-responsive element modulator | log2 fold change | 1.229 | 0.1191 | 9.019e-22 | Study-level association; see design caveats |
PRJNA852380 — pathogen challenge
Study design, replication and limitations
No phenotype is deposited; AREE records the digestive-gland transcriptional response to Vibrio exposure.
Records: 20,792; genes with nonmissing raw p-values: 20,766. Study-level associations.
Adjusted p < 0.05: 3,296 (1,816 positive, 1,480 negative). Counts are study-level molecular associations.
Biological replication: 6 digestive-gland libraries: 3 controls and 3 at 24 h after Vibrio exposure. Each library is a pool by expressed-SNP genotype; pool size is not recorded.
Treatment: Exposed to Vibrio and sampled 24 h later (species, dose and route not stated in the metadata)
Control: Unexposed control oysters
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
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| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105349013 | superoxide dismutase [Cu-Zn]-like | log2 fold change | -4.071 | 0.2137 | 1.336e-76 | Study-level association; see design caveats |
| NCBI:GeneID:105349071 | arylsulfatase B | log2 fold change | 2.998 | 0.196 | 7.767e-49 | Study-level association; see design caveats |
| NCBI:GeneID:105345603 | putative peptidyl-prolyl cis-trans isomerase | log2 fold change | 1.822 | 0.1357 | 2.787e-37 | Study-level association; see design caveats |
| NCBI:GeneID:105321376 | EF-hand calcium-binding domain-containing protein 1 | log2 fold change | 5.007 | 0.3741 | 3.533e-37 | Study-level association; see design caveats |
| NCBI:GeneID:105319128 | chromobox protein homolog 8 | log2 fold change | 2.42 | 0.1992 | 2.184e-30 | Study-level association; see design caveats |
| NCBI:GeneID:105332697 | midasin | log2 fold change | 1.592 | 0.137 | 1.015e-27 | Study-level association; see design caveats |
| NCBI:GeneID:105334682 | kelch-like protein 24 | log2 fold change | 1.127 | 0.09977 | 3.688e-26 | Study-level association; see design caveats |
| NCBI:GeneID:105318810 | uncharacterized LOC105318810 | log2 fold change | -3.029 | 0.2856 | 6.601e-23 | Study-level association; see design caveats |
| NCBI:GeneID:105323667 | metalloproteinase inhibitor 2-like | log2 fold change | 1.696 | 0.1633 | 5.554e-22 | Study-level association; see design caveats |
| NCBI:GeneID:105327361 | protein arginine N-methyltransferase 1 | log2 fold change | 1.537 | 0.148 | 5.554e-22 | Study-level association; see design caveats |
PRJNA515169 — pathogen challenge
Study design, replication and limitations
Virulent V. tasmaniensis LGP32 killed about 60% of oysters within 3 days, through phagocytosis-dependent hemocyte lysis requiring intracellular T6SS effectors. AREE records the 8 h whole-spat transcriptional response to infection, not survival per library.
Records: 23,984; genes with nonmissing raw p-values: 23,984. Study-level associations.
Adjusted p < 0.05: 489 (397 positive, 92 negative). Counts are study-level molecular associations.
Biological replication: 6 libraries, each a pool of 30 spat: one mock and one V. tasmaniensis LGP32 pool from each of three independent infection experiments. Pools of 30 animals average out individual variation, so replication is at the level of experiments.
Treatment: Injected into the adductor muscle with 7.5 x 10^7 CFU of the virulent Vibrio tasmaniensis LGP32 and sampled 8 h later
Control: Mock-injected with sterile seawater and sampled 8 h later (sample alias ‘anesthesis’)
Positive effects indicate higher expression in the treatment relative to the control; negative effects indicate lower expression.
Download all harmonized evidence
| Feature / card | RefSeq description | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|
| NCBI:GeneID:105321376 | EF-hand calcium-binding domain-containing protein 1 | log2 fold change | 3.494 | 0.1231 | 5.862e-173 | Study-level association; see design caveats |
| NCBI:GeneID:136273704 | coadhesin-like | log2 fold change | 3.102 | 0.1597 | 4.387e-80 | Study-level association; see design caveats |
| NCBI:GeneID:136270488 | uncharacterized LOC136270488 | log2 fold change | 3.462 | 0.1858 | 9.012e-74 | Study-level association; see design caveats |
| NCBI:GeneID:105342241 | hypothetical protein | log2 fold change | 4.689 | 0.289 | 1.381e-55 | Study-level association; see design caveats |
| NCBI:GeneID:136273062 | galanin receptor 2b-like | log2 fold change | 2.186 | 0.1418 | 4.049e-50 | Study-level association; see design caveats |
| NCBI:GeneID:105318026 | tumor necrosis factor receptor superfamily member 11A | log2 fold change | 2.742 | 0.1817 | 4.608e-48 | Study-level association; see design caveats |
| NCBI:GeneID:136276560 | uncharacterized LOC136276560 | log2 fold change | 3.952 | 0.2636 | 1.835e-47 | Study-level association; see design caveats |
| NCBI:GeneID:105321692 | cytochrome P450 2C31-like | log2 fold change | 2.503 | 0.1759 | 1.112e-42 | Study-level association; see design caveats |
| NCBI:GeneID:105332146 | serum amyloid A-5 protein | log2 fold change | 2.626 | 0.1901 | 3.88e-40 | Study-level association; see design caveats |
| NCBI:GeneID:105320131 | prostaglandin E2 receptor EP4 subtype | log2 fold change | 2.449 | 0.1786 | 1.432e-39 | Study-level association; see design caveats |