Evidence card: NCBI:GeneID:105344432
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 |
|---|---|---|---|---|---|---|---|
| CGIG_PESTO_F0_RNASEQ_PRJEB58194 | M-phase inducer phosphatase | pesticide_mixture_0_48hpf_vs_control_F0_gastrula_dlarva | log2 fold change | 1.898 | 0.3138 | 7.107e-06 | Study-level association; see design caveats |
| CGIG_PESTO_F1DIRECT_RNASEQ_PRJEB58194 | M-phase inducer phosphatase | pesticide_mixture_TE_vs_TT_F1_gastrula_pediveliger | log2 fold change | -1.386 | 0.814 | 1 | Study-level association; see design caveats |
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.