Evidence card: NCBI:GeneID:136276238

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
PRJEB18614	uncharacterized LOC136276238	alexandrium_minutum_vs_heterocapsa_triquetra_diet	log2 fold change	0.2475	0.4302	not available	Study-level association; see design caveats
PRJNA298285	uncharacterized LOC136276238	pH7.9_vs_pH8.1_20C_larvae	log2 fold change	0.6331	0.1014	4.124e-06	Study-level association; see design caveats
PRJNA826964	uncharacterized LOC136276238	ocean_acidification_vs_ambient_control	log2 fold change	0.1918	0.957	0.976	Study-level association; see design caveats
PRJNA1329250	uncharacterized LOC136276238	oshv1_microvariant_challenge_vs_unchallenged_control	log2 fold change	1.135	0.4158	not available	Study-level association; see design caveats
CGIG_PESTO_F0_RNASEQ_PRJEB58194	uncharacterized LOC136276238	pesticide_mixture_0_48hpf_vs_control_F0_gastrula_dlarva	log2 fold change	-0.8473	0.5122	0.4149	Study-level association; see design caveats
CGIG_PESTO_F1DIRECT_RNASEQ_PRJEB58194	uncharacterized LOC136276238	pesticide_mixture_TE_vs_TT_F1_gastrula_pediveliger	log2 fold change	-0.1248	0.2727	1	Study-level association; see design caveats
PRJNA694496	uncharacterized LOC136276238	thermotolerance_selected_vs_nonselected_control	log2 fold change	1.306	0.3586	0.001232	Study-level association; see design caveats

CGIG_HAB_RNASEQ_PRJEB18614

Phenotype interpretation: 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.

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.

Evidence classification: stress_response. Tissue: gill; life stage: adult.

Quality flags: raw_reanalysis;harmful_algal_bloom_response;time_averaged_over_diurnal_cycle;timepoint_blocked_contrast;sequencing_pool_partly_confounded;deseq2_significance_unavailable.

Study limitations:

Each library was sequenced on two lanes; the lanes are technical duplicates of one library, not replicates. Only the lower-numbered lane of each pair is used (26 of the 52 deposited runs, 136.8 GB instead of about 274 GB). The unused run is named in each manifest row.
Reads come from two mirrors. 12 runs are the ENA FASTQs, checked against the manifest MD5s. The other 14, listed with NCBI’s size and MD5 in CGIG_HAB_RNASEQ_PRJEB18614_sra_locations.tsv, were converted from full NCBI .sra archives, and their read counts were checked against the manifest. They were moved to NCBI after ENA corrupted multi-connection transfers and then refused requests. Each library comes from one mirror only.
Both day 2 ZT 8.5 gill pools (control and A. minutum) carry adductor-muscle RNA from dissection and are excluded from the primary contrast; sample_size counts the 24 remaining pools. The all-26 fit is kept as a comparison.
Salmon detected one ENA library (control d1 ZT 12.5, ERR1758944) as ISF instead of the ISR expected for stranded TruSeq, so its read files are swapped relative to the rest. Library type is inferred per sample, so quantification is unaffected.
The primary contrast, ~ timepoint + condition, blocks on sampling time and uses 12 time-matched pools per diet after excluding the contaminated pair. The all-26 sensitivity model and publication use 13 per diet. The publication’s central finding is that A. minutum remodels the daily cycling of gill transcripts, so a diet effect averaged over time will miss, or dilute, effects confined to part of the cycle.
Diet is partly confounded with sequencing pool. The libraries were multiplexed into four pools, each on its own lane pair of one flowcell. Pool L003-L004 holds 6 A. minutum libraries and no controls, and pool L005-L006 holds 6 controls and 1 A. minutum library; pools L001-L002 and L007-L008 carry both diets. The sensitivity model with sequencing_pool as a covariate keeps the direction of 99.9% of the primary significant genes, including all 30 top genes, which also stay significant. Only 53.8% of genes overall stay significant, so the gene count depends on the model, but the direction does not.
Each diet used three tanks, but the publication does not say how the 6 oysters in each pool were drawn from them, so tank effects cannot be modelled.
Timepoint labels are Day and Zeitgeber time rounded down: d1_zt04 is Day 1 ZT 4.5 and d3_zt04 is Day 3 ZT 4.5, where ZT 0 is lights on. The methods list the same 13 times as the ArrayExpress SDRF.
Condition, time and lane come from the ArrayExpress E-MTAB-5345 SDRF (feeding condition, time and assay name), and every ENA sample alias matches its SDRF source name.
The publication aligned reads with STAR to the Ensembl Metazoa C. gigas genome and mitochondrial genome and tested diet with edgeR across the 13 times, reporting 740 differentially expressed transcripts at FDR < 0.01 (89.5% higher under A. minutum). The transcript list is not in the supplement, whose only table lists the 30 most significant cycling transcripts per class, so only the count and direction balance can be compared. AREE finds about 5,070 genes at FDR < 0.01, 59.6% higher under A. minutum. That is far more genes and a weaker up-bias than the published 740 transcripts (89.5% up), with a different aligner, count model and genome assembly.
The strongest A. minutum-higher genes form a lysosomal and endocytic programme (dipeptidyl peptidase 1, LAMP1, CD63, VPS4B, syntaxin-8) and include detoxification genes: the ABCB1 multidrug efflux pump, arylacetamide deacetylase and mitochondrial alternative oxidase.

Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.

Harmonized evidence. Processed input. Input SHA-256: 185cbdd6f509f43a79442fe2fd9137ea489711c4afe95d0f2a1a21c6c6b4762a.

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;fdr_lt_0.05.

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_OA_RNASEQ_PRJNA826964

Phenotype interpretation: 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

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

Evidence classification: stress_response. Tissue: hepatopancreas; life stage: not_recorded.

Quality flags: raw_reanalysis;ocean_acidification_response;timepoint_blocked_contrast;pooled_rna_samples;possible_genetic_background_confound.

Study limitations:

No publication is linked to the BioProject, and searches of PubMed, Europe PMC full text and Crossref on 2026-09-28 found none, so there are no published methods, results or effect tables to reconcile the reanalysis against.
The acidification intensity (target pH or pCO2), seawater carbonate chemistry, temperature and oyster size or age are not recorded in the public metadata, so exposure intensity and life stage are unresolved.
The treatment was probably CO2-driven acidification to pH 7.50. This is inferred, not documented: the same IOCAS group (L. Qiu and colleagues) ran C. gigas CO2 exposures at pH 7.50 sampled from 7 to 56 days (Wang et al. 2021, Ecotoxicol Environ Saf, doi:10.1016/j.ecoenv.2021.112235) and at pH 7.50 for 7 and 60 days (Wang et al. 2020, Sci Total Environ, doi:10.1016/j.scitotenv.2020.140177), and reported hepatopancreas responses to acidification over about two months (Zhang et al. 2021, J Oceanol Limnol, doi:10.1007/s00343-021-0462-x). None of these papers is linked to PRJNA826964, and the closed-access hepatopancreas paper, the most likely companion, has not been checked against it.
The primary AREE contrast compares the three acidified pools with the three control pools and blocks on sampling day (~ timepoint + condition); it estimates an acidification effect averaged over 7, 28 and 56 days rather than time-specific or acclimation effects, and it has only two residual degrees of freedom.
The three libraries per day-by-condition cell are technical replicates of one pooled RNA sample, not the independent biological replicates the BioSample attributes state. Expressed-SNP allele frequencies (scripts/check_replicate_genotypes.py, 4M read pairs per library) agree within a cell to within resequencing noise and show no single-animal genotype peaks, and within-cell expression dispersion is 2.7% BCV against 10.8-22.4% in the other AREE oyster studies. Treating the 18 libraries as replicates inflates significance roughly twelvefold, so the libraries are summed into 6 pools (–collapse-by=condition+timepoint).
Each pool is a different set of animals, and the acidified pools are genetically further from the controls (mean allele-frequency difference 0.24-0.31) than the control pools are from one another (0.085-0.19), so acidified and control oysters may come from different stocks or families. Several of the strongest effects are 4-6 log2 changes in transposon-derived genes (tigger, HARBI1), the pattern expected from presence-absence variation between genetic backgrounds, so part of the contrast may be genetic rather than an acidification response. The evidence is harmonized with every row flagged pooled_rna_samples and possible_genetic_background_confound, so scoring discounts it and evidence cards list the caveat; treat it as provisional acidification evidence until a design with shared genetic backgrounds confirms it.
Condition, sampling day and replicate were taken from NCBI BioSample treatment and replicate attributes and agree with the library names (C/O = control/acidified, followed by day and replicate).
The BioProject carries no author-deposited processed expression matrix.

Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.

Harmonized evidence. Processed input. Input SHA-256: 4a01845d837665c4e977190e7e9111a2d5a7bd3e5f38d89ca473276a96b26f2c.

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.

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.

CGIG_THERMOTOL_RNASEQ_PRJNA694496

Phenotype interpretation: Selected population had higher post-heat-shock survival (78.05% versus 66.34%) and field summer survival (73% versus 62%)

Biological replication: RNA-seq: 3 selected-population and 3 control-population larval libraries; number of larvae pooled per library was not reported

Evidence classification: resilience_associated. Tissue: whole_larva; life stage: umbo_larva.

Quality flags: raw_reanalysis;qc_reviewed;population_selection_association;constitutive_expression;selected_A_pc2_displacement;sensitivity_direction_robust;fdr_lt_0.05.

Study limitations:

The RNA-seq comparison is constitutive selected-versus-control expression at the larval stage, not an acute heat-versus-control contrast.
Thermotolerance survival was measured in related later-stage cohorts rather than the RNA-sequenced larval pools.
The publication reports 4,764 DEGs but does not provide the complete feature-level effect, p-value, or standard-error table in its supplementary archive.
The publication describes three replicates per group but does not report how many larvae were pooled into each RNA-seq library.
All six runs share one BioSample record, and its tissue field says gill despite the publication consistently describing whole umbo larvae; AREE follows the publication for tissue and records the discrepancy.
The source genome assembly and differential-expression software/threshold are not reported clearly enough for exact reproduction; AREE used GCF_963853765.1/RS_2024_06, so these results are a current-reference reanalysis rather than an exact reconstruction of the publication pipeline.
Selected_B and selected_C have lower Salmon mapping rates than the other libraries, and selected_A is displaced on PC2; sensitivity analysis supports the primary effect directions, but these patterns remain QC caveats.

Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.

Harmonized evidence. Processed input. Input SHA-256: 636f73eb2b9094e50a8c3c3213792513bff4e26fc203a607471190188445b6a3.

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.