Evidence card: NCBI:GeneID:136270694
Real public-study evidence. Association evidence only; not a validated biomarker.
How to interpret expression as evidence for resilience. Differential expression alone does not establish a resilience marker; higher expression does not necessarily mean greater resilience.
This feature was selected among up to ten displayed findings in at least one study. All available rows for it are shown below, including nonsignificant and exploratory results. Presence in multiple datasets does not establish independent replication: exposures, tissues, life stages, and phenotype meanings differ. No cross-study score or pooled effect is calculated.
Guide to effect sizes, uncertainty and gene descriptions.
Study-specific effects
| Study / design | RefSeq description | Contrast | Effect scale | Effect | Standard error | Adjusted p-value | Interpretation |
|---|---|---|---|---|---|---|---|
| PRJNA298285 | eggshell protein-like | pH7.9_vs_pH8.1_20C_larvae | log2 fold change | 0.3221 | 0.2015 | 0.9541 | Study-level association; see design caveats |
| PRJNA1329250 | eggshell protein-like | oshv1_microvariant_challenge_vs_unchallenged_control | log2 fold change | -0.4871 | 0.3109 | not available | Study-level association; see design caveats |
| CGIG_PESTO_F0_RNASEQ_PRJEB58194 | eggshell protein-like | pesticide_mixture_0_48hpf_vs_control_F0_gastrula_dlarva | log2 fold change | -2.098 | 0.3616 | 2.534e-05 | Study-level association; see design caveats |
| CGIG_PESTO_F1DIRECT_RNASEQ_PRJEB58194 | eggshell protein-like | pesticide_mixture_TE_vs_TT_F1_gastrula_pediveliger | log2 fold change | -0.2609 | 0.4865 | 1 | Study-level association; see design caveats |
CGIG_LARVAL_OA_RNASEQ_PRJNA298285
Phenotype interpretation: No phenotype is deposited and no publication is linked; AREE records the larval transcriptional response averaged over three developmental stages.
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.
Evidence classification: environmental_exposure. Tissue: whole_organism; life stage: larva.
Quality flags: raw_reanalysis;larval_development;pooled_libraries;stage_blocked_contrast;shared_control_group;dependence_group=PRJNA298285_ambient_larvae;no_linked_publication;ocean_acidification_response;replicate_culture_independence_unverified.
Study limitations:
- No publication is linked to the BioProject, and searches of PubMed and Europe PMC (including the accessions PRJNA298285 and SRP064660) on 2026-10-07 found none, so there are no published methods, carbonate chemistry, survival data or results to reconcile against.
- The three AREE records from this study (acidified, warmed, acidified + warmed) test against the same six ambient libraries, so they carry the dependence group PRJNA298285_ambient_larvae and count as one replication group.
- There are two libraries per stage and treatment. The stage block (~ stage + condition) treats them as replicates; whether they come from separate cultures is not recorded and is checked with scripts/check_replicate_genotypes.py.
- The treatments are mild (pH 7.9 against 8.1; 22 C against 20 C), so small transcriptional effects are expected.
- Treatment, stage and replicate come from the ENA sample aliases (C.gigas_
) and library names ( <Trc | Vg1 | Vg2>_<ambi | acid | warm | intr><A | B>), and agree with the BioSample pH, temperature, dev_stage and age attributes. One library name is a file name (C3759_TAGCTT_L003_R1_001.fastq.gz, late-veliger warmed); it is taken as replicate B because the other late-veliger warmed library is C3752_Vg2_warmA. One library (D5236_Trc_warmA) is from a later sequencing batch at 126 bp. - All runs come from NCBI .sra archives checked against NCBI’s MD5s, with read counts checked against the manifest on conversion.
- The A and B libraries of each cell have nearly identical expression profiles and cannot be distinguished genetically from libraries of other treatments, so they may be subsamples of one culture; if so, the error model understates variability and significance is optimistic. The record carries the flag replicate_culture_independence_unverified.
Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.
Harmonized evidence. Processed input. Input SHA-256: 2bae06ceaff293aaaa0e3dbf9ec6cce42ea0b18c4028ba6ef4e2a374cfeee32b.
CGIG_OSHV1_RNASEQ_PRJNA1329250
Phenotype interpretation: 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
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)
Evidence classification: disease_associated. Tissue: whole_soft_tissue; life stage: spat.
Quality flags: raw_reanalysis;pathogen_challenge_response;lineage_balanced_contrast;deseq2_significance_unavailable.
Study limitations:
- This intake represents the molecular antiviral response to experimental OsHV-1 microvariant challenge, not a measured survival or organism-level disease-resistance difference between the two lineages.
- Challenge dose, exposure duration, and time of sampling after inoculation are not recorded in the public SRA metadata, so exposure intensity and duration are unresolved.
- The challenged and control arms are unequal in size (30 versus 12 libraries), but lineage is balanced within each arm and within every viral strain: 6 Midori and 6 Miyagi controls, and 5 of each lineage for each of the Australia, France, and USA strains. The lineage effect is therefore not confounded with infection status, and AREE blocks on lineage as ~ population + condition.
- The publication contrasts the USA and Australia microvariant strains and reports no marked difference between them; the France-strain libraries are present in the BioProject and are pooled into the challenged arm of the AREE contrast rather than analyzed as a separate strain effect.
- The BioProject carries no author-deposited processed expression matrix, so AREE has no published feature-level effect table to reconcile against.
- Condition, lineage, and viral-strain assignments were reconstructed from NCBI BioSample attribute tags rather than from a supplementary sample table; the source metadata spells the Miyagi lineage ‘Myagi’, which AREE normalized.
Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.
Harmonized evidence. Processed input. Input SHA-256: 3beb15844b8040ff58c64acd452381f853bbbacb730cce2bf434b6ee05d41f2e.
CGIG_PESTO_F0_RNASEQ_PRJEB58194
Phenotype interpretation: 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.
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.
Evidence classification: environmental_exposure. Tissue: whole_organism; life stage: embryo_larva.
Quality flags: raw_reanalysis;pollutant_exposure_response;pesticide_mixture;pooled_libraries;stage_blocked_contrast;direct_exposure;fdr_lt_0.05.
Study limitations:
- One control D-larva sample title (BT2Ed) is attached to two runs (ERR10659105, ERR10659106); both are kept with the run accession appended to the replicate, and the expressed-SNP check tests whether they are one sample.
- The exposure is a mixture of 18 pesticides and metals at environmentally relevant concentration (nominal sum 2.85 ug/L; measured 3.74 ug/L in F0) during embryo-larval development (0-48 h post fertilization) at the Ifremer Bouin hatchery.
- Each library is presumably a pool of many embryos or larvae; pool size, culture vessels and the meaning of the F0 group digits (1-3) are not recorded in the public metadata, and pools were checked with the expressed-SNP test (scripts/check_replicate_genotypes.py) before analysis.
- All runs come from NCBI .sra archives checked against NCBI’s MD5s (11 F0 runs have no ENA FASTQ), with read counts checked against the NCBI spot counts on conversion.
- The study also deposited F0 pediveligers (sampled after exposure) and F1 offspring exposed in both generations (EE); AREE does not use them.
Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.
Harmonized evidence. Processed input. Input SHA-256: 5eb3fa1130b516be240eecebcd8c88a5b405a6739f99d273764f3054814af5bb.
CGIG_PESTO_F1DIRECT_RNASEQ_PRJEB58194
Phenotype interpretation: 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.
Biological replication: 12 libraries: 6 TT and 6 TE, three per stage.
Evidence classification: environmental_exposure. Tissue: whole_organism; life stage: embryo_larva.
Quality flags: raw_reanalysis;pollutant_exposure_response;pesticide_mixture;pooled_libraries;stage_blocked_contrast;shared_control_group;dependence_group=PRJEB58194_F1_TT;direct_exposure.
Study limitations:
- The two F1 records (direct exposure TE and parental exposure ET) test against the same six TT libraries, so they carry the dependence group PRJEB58194_F1_TT; only the direct-exposure record is harmonized.
- The exposure is a mixture of 18 pesticides and metals at environmentally relevant concentration (nominal sum 2.85 ug/L; measured 3.74 ug/L in F0) during embryo-larval development (0-48 h post fertilization) at the Ifremer Bouin hatchery.
- Each library is presumably a pool of many embryos or larvae; pool size, culture vessels and the meaning of the F0 group digits (1-3) are not recorded in the public metadata, and pools were checked with the expressed-SNP test (scripts/check_replicate_genotypes.py) before analysis.
- All runs come from NCBI .sra archives checked against NCBI’s MD5s (11 F0 runs have no ENA FASTQ), with read counts checked against the NCBI spot counts on conversion.
- The study also deposited F0 pediveligers (sampled after exposure) and F1 offspring exposed in both generations (EE); AREE does not use them.
Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.
Harmonized evidence. Processed input. Input SHA-256: eeb95c68cdb8cacd7c256a0616f24042aaa54da88a33682cf82f476119e25b62.
Next validation step
Independent biological replication with matched exposure and measured phenotype, an appropriate experimental-unit model, and targeted validation in the relevant tissue and life stage.