Real-study intake: PRJNA516762
Scope
- Study: Liu et al. (2019), RNAi based transcriptome suggests genes potentially regulated by HSF1 in the Pacific oyster Crassostrea gigas under thermal stress.
- DOI: https://doi.org/10.1186/s12864-019-6003-8
- Raw-data accessions: BioProject
PRJNA516762; SRA studySRP181984; 12 paired-end Illumina HiSeq X Ten runs. - AREE contrast: untreated control versus 35 C heat shock for 2 h, excluding the HSF1 RNAi arms.
- Biological replication for this contrast: 3 pooled libraries per condition, each pooling 5 oysters (30 oysters represented in 6 libraries).
Processed-result QC
- The publication reports 150 significant genes for the direct heat-versus-control contrast; the source workbook and derived AREE table both contain 150 records.
- Direction counts: 76 upregulated and 74 downregulated.
- All reported directions agree with the sign of the published log2 fold change.
- FDR range:
3.0261e-86to0.049902; all records satisfy the publication’s FDR threshold. - Raw p-values and standard errors are not available in the supplement and remain null in AREE.
- Mapping release
cgigas_cgi_to_ncbi_gene_rs2024_06_v1resolves 60 of 150 features (40.0%) to 60 unique NCBI Gene IDs in RefSeq annotationGCF_963853765.1-RS_2024_06; all resolved mappings are conservatively labeledinferred. - Among the 112 published
CGI_*identifiers, 60 (53.6%) resolve. The other 90 total features retain their original identifiers with confidenceunresolvedand must not be collapsed across studies.
Largest published effects
| Direction | Feature | log2 fold change | FDR |
|---|---|---|---|
| Up | CGI_10002387 (NCBI:GeneID:105327207) |
4.3219 | 3.0261e-86 |
| Up | CGI_10002823 |
2.0048 | 1.1331e-10 |
| Up | CGI_10009093 |
1.8845 | 2.3745e-14 |
| Up | CGI_10002068 |
1.8766 | 1.5230e-09 |
| Up | CGI_10002950 |
1.8217 | 1.2167e-14 |
| Down | CGI_10020949 |
-3.5236 | 1.9524e-37 |
| Down | CGI_10018182 |
-2.7578 | 7.1855e-24 |
| Down | CGI_10001445 |
-2.5893 | 1.8609e-18 |
| Down | CGI_10010392 |
-2.4298 | 1.0999e-22 |
| Down | CGI_10016700 |
-2.3808 | 1.1136e-15 |
Interpretation guardrail
These are significant molecular heat-response associations from a pooled, single-study contrast. The experiment did not directly measure survival or organism-level thermal tolerance, so these records are classified as stress_response, not validated resilience biomarkers.
Next analytical step
Curate an independent thermal-challenge study with compatible feature identifiers and effect uncertainty. For the 90 unresolved features, add sequence- or transcript-level mapping evidence rather than relaxing the coordinate thresholds. Random-effects meta-analysis should wait until at least two independent studies have standardized identifiers and usable uncertainty estimates; this supplement does not report standard errors.