PRJNA298285 RefSeq functional annotations

Descriptions and gene biotypes come directly from GCF_963853765.1 / RS_2024_06. This is annotation and ranking, not ontology or pathway enrichment.

Acidified Higher Fdr Lt 0.05

Genes: 25; RefSeq-characterized descriptions: 10 (40.0%).

  • LOC105336939 (NCBI:GeneID:105336939): early endosome antigen 1 (log2FC=0.49; adjusted p=0.00047)
  • LOC105324334 (NCBI:GeneID:105324334): carnosine synthase 1 (log2FC=0.33; adjusted p=0.00531)
  • LOC105345814 (NCBI:GeneID:105345814): CCAAT/enhancer-binding protein beta (log2FC=0.33; adjusted p=0.00643)
  • LOC105348950 (NCBI:GeneID:105348950): RNA-binding protein RO60 (log2FC=0.25; adjusted p=0.0205)
  • LOC105332757 (NCBI:GeneID:105332757): POTE ankyrin domain family member B (log2FC=0.50; adjusted p=0.0205)
  • LOC105338425 (NCBI:GeneID:105338425): histone H3.3A (log2FC=0.35; adjusted p=0.0205)
  • LOC105344043 (NCBI:GeneID:105344043): cytochrome P450 2C8 (log2FC=0.33; adjusted p=0.022)
  • LOC105318670 (NCBI:GeneID:105318670): shematrin-like protein 1 (log2FC=0.72; adjusted p=0.0222)
  • LOC105318255 (NCBI:GeneID:105318255): NF-kappa-B inhibitor epsilon-like (log2FC=0.36; adjusted p=0.0225)
  • LOC105329925 (NCBI:GeneID:105329925): cytochrome P450 2B4 (log2FC=0.75; adjusted p=0.0492)

Acidified Lower Fdr Lt 0.05

Genes: 13; RefSeq-characterized descriptions: 5 (38.5%).

  • LOC105340879 (NCBI:GeneID:105340879): mucin-2 (log2FC=-0.52; adjusted p=0.00643)
  • LOC105347527 (NCBI:GeneID:105347527): sodium- and chloride-dependent glycine transporter 1 (log2FC=-0.24; adjusted p=0.0205)
  • LOC105343143 (NCBI:GeneID:105343143): b(0,+)-type amino acid transporter 1 (log2FC=-0.26; adjusted p=0.0295)
  • LOC105320220 (NCBI:GeneID:105320220): beta-hexosaminidase (log2FC=-0.81; adjusted p=0.0312)
  • LOC105326540 (NCBI:GeneID:105326540): prisilkin-39 (log2FC=-0.46; adjusted p=0.0312)

Gene-biotype over-representation

One-sided hypergeometric tests compare each significant direction with all genes having DESeq2 results; Benjamini-Hochberg adjustment covers both directions and all biotypes.

  • acidified higher fdr lt 0.05: lncRNA (9 observed, 2.1 expected; fold=4.24; adjusted p=0.00182)

Many oyster loci retain automated or uncharacterized RefSeq labels. Functional claims should be based on formal ontology/pathway enrichment or orthology-aware analysis rather than names alone.