Evidence card: NCBI:GeneID:105338552

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
PRJEB86646	uncharacterized LOC105338552	30C_vs_23C_fed_before_oshv1	log2 fold change	0.3124	0.698	0.7767	Study-level association; see design caveats
PRJNA298285	uncharacterized LOC105338552	pH7.9_vs_pH8.1_20C_larvae	log2 fold change	-0.4917	0.301	0.9541	Study-level association; see design caveats
PRJNA735889	uncharacterized LOC105338552	ph_6.5_6.8_vs_ph_7.4_7.8_23d_juveniles	log2 fold change	0.06199	0.7351	0.9718 (nominal only)	Exploratory; tank clustering unmodeled
CGIG_PESTO_F0_RNASEQ_PRJEB58194	uncharacterized LOC105338552	pesticide_mixture_0_48hpf_vs_control_F0_gastrula_dlarva	log2 fold change	-0.0428	0.242	0.9567	Study-level association; see design caveats
CGIG_PESTO_F1DIRECT_RNASEQ_PRJEB58194	uncharacterized LOC105338552	pesticide_mixture_TE_vs_TT_F1_gastrula_pediveliger	log2 fold change	0.5188	0.1763	0.535	Study-level association; see design caveats
PRJNA694496	uncharacterized LOC105338552	thermotolerance_selected_vs_nonselected_control	log2 fold change	-3.126	0.1263	2.561e-131	Study-level association; see design caveats

CGIG_HEAT_RNASEQ_PRJEB86646

Phenotype interpretation: 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.

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.

Evidence classification: resilience_associated. Tissue: whole_soft_tissue; life stage: spat.

Quality flags: raw_reanalysis;temperature_response;pre_infection_baseline;family_blocked_contrast;shared_control_group_with_PRJEB86618;dependence_group=DECICOMP_PRJEB86525_0h_controls.

Study limitations:

The six 23 C fed control libraries (PRJEB86525, 0 h) are the same libraries used as controls in CGIG_STARVATION_RNASEQ_PRJEB86618. The two harmonized studies therefore share a reference group, so their effect estimates are correlated and must not be treated as independent in a meta-analysis.
The contrast uses only the 0 h libraries, sampled when the OsHV-1 mu-Var donors were added, so it captures temperature without infection. The 36 later libraries (3-72 h) follow infection, which progresses far less at 30 C, and are not used.
Each tank held both families, so the F11N and F14R libraries with the same replicate number probably share a tank. The model ~ family + condition treats the six libraries per temperature as independent, although only three tanks per temperature are independent units.
The 30 C arm and the 23 C controls were held in separate tanks of one experiment at the Argenton station, so tank is nested in temperature.
Condition, family, time and replicate come from the ENA sample aliases and titles (sam_P_<3 fed 23 C | 4 fed 30 C>_), and the two sources agree for every library.
The publication reports enhanced baseline antiviral immunity at 30 C. At 0 h this reanalysis finds the opposite for several classic antiviral markers: all 13 significant interferon-induced protein 44 genes, 10 of 12 significant tumor necrosis factor genes and both significant 2’-5’-oligoadenylate synthetase genes are lower at 30 C. The publication is not open access and its gene lists were not compared, so whether this reflects different gene sets, a different time point or a real disagreement is unresolved.
Pools at 30 C map about three points less to the transcriptome than pools at 23 C. The shift is systematic but small beside the expression effects.

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

Harmonized evidence. Processed input. Input SHA-256: abbc33a2dc6e48a0f0a903bbca1d4bce3f90c56927e80ff5c5bc3e88dd6c0c5c.

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_OA_RNASEQ_PRJNA735889

Phenotype interpretation: 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

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.

Evidence classification: environmental_exposure. Tissue: whole_organism; life stage: juvenile.

Quality flags: raw_reanalysis;ocean_acidification_response;ph_band_contrast_tipping_window_excluded;no_ambient_ph_reference;one_tank_per_ph_level;gametogenesis_blocked_contrast;exploratory_tank_clustering_unmodeled.

Exploratory uncertainty: Tank clustering is unmodeled. Standard errors and adjusted p-values above are nominal only; this row is excluded from pooling and significance rewards.

Study limitations:

The study is a 15-level pH gradient (pHT 6.5-7.8, 76 libraries). AREE reduces it to a two-group contrast at the authors’ tipping-point window: the five tanks inside pHT 7.3-6.9 (tanks 1, 6, 4, 11 and 10; 25 libraries) are excluded and not downloaded. Effect sizes are therefore log2 fold changes between two pH bands, not slopes per pH unit, and they mix the response across five pH levels on each side.
There is no ambient-pH tank; the reference band (pHT 7.4-7.8) is itself below present-day coastal pH, so the contrast understates the full response to acidification.
Each pH level is a single tank, so tank and pH are confounded at the level of a single pH; with five tanks per band the band contrast has tank-level replication, but DESeq2 treats the 50 analysed oysters as independent and does not model tank. Standard errors, p-values and FDR values are exploratory and may overstate precision. A tank-aware reanalysis is required before inferential use; PCA and per-tank residual checks do not correct the error model.
Tank 15 is labelled ‘pHT 6.5 bis’ in BioSample: a second tank at pHT 6.5 alongside tank 9.
Library 13Ebis (SRR14803132) has a different index from 13E (SRR14803133) and about half its reads. The expressed-SNP check shows it is the same oyster (allele-frequency difference 0.026, below the 0.032 expected for one RNA resequenced; the next closest pair differs by 0.198), so it is kept in the manifest but left out of the analysis.
Male gametogenesis is unbalanced between bands: a spermatogenesis module is active in 11 of 25 control and 2 of 25 acidified oysters (Fisher p = 0.008), spread across all five control tanks, which suggests that low pH delays or suppresses the onset of spermatogenesis in 5-month-old juveniles. The primary model blocks on this call (~ gametogenesis + condition) so the evidence records a gametogenesis-adjusted association with pH, without establishing a direct causal response; the unadjusted model is kept as a sensitivity analysis. The call is a transcriptional proxy derived from the same data (scripts/score_prjna735889_gametogenesis.py), not a histological sex or maturation call, and with only two active acidified oysters the gametogenesis effect is estimated mostly from the control band.
Condition, tank and pH come from the NCBI BioSample title, treatment and growth_protocol attributes; every library is paired-end. ENA served the FASTQs at about 80 KB/s on 2026-10-02, so all 51 runs are taken from the NCBI Open Data mirror as .sra archives checked against the size and MD5 NCBI publishes (CGIG_OA_RNASEQ_PRJNA735889_sra_locations.tsv), and each converted FASTQ pair must match the manifest read count.

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

Harmonized evidence. Processed input. Input SHA-256: a8f7485ec9436cc334d22b6819d7137f37dccb753fa688700c49d264cb7c0dda.

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.