PRJNA735889 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: 2,735; RefSeq-characterized descriptions: 1,872 (68.4%).

  • LOC105339377 (NCBI:GeneID:105339377): monocarboxylate transporter 12 (log2FC=3.17; adjusted p=1.35e-26)
  • LOC105332517 (NCBI:GeneID:105332517): BPTI/Kunitz domain-containing protein-like (log2FC=6.53; adjusted p=8.4e-19)
  • LOC105340069 (NCBI:GeneID:105340069): circumsporozoite protein (log2FC=2.73; adjusted p=2.22e-16)
  • LOC105334853 (NCBI:GeneID:105334853): mesenchyme-specific cell surface glycoprotein (log2FC=3.14; adjusted p=3.04e-15)
  • LOC105326383 (NCBI:GeneID:105326383): selenoprotein F-like (log2FC=0.48; adjusted p=2.2e-13)
  • LOC105335780 (NCBI:GeneID:105335780): splicing factor U2AF 50 kDa subunit (log2FC=0.44; adjusted p=4.28e-13)
  • LOC105344631 (NCBI:GeneID:105344631): endothelin-converting enzyme 1 (log2FC=1.51; adjusted p=1.08e-12)
  • LOC105332521 (NCBI:GeneID:105332521): eppin (log2FC=3.69; adjusted p=1.22e-12)
  • LOC105327851 (NCBI:GeneID:105327851): serine/arginine-rich splicing factor 1A (log2FC=0.32; adjusted p=1.6e-12)
  • LOC105334576 (NCBI:GeneID:105334576): coatomer subunit epsilon (log2FC=0.43; adjusted p=1.85e-11)
  • LOC105327473 (NCBI:GeneID:105327473): ileal sodium/bile acid cotransporter (log2FC=2.32; adjusted p=4.12e-11)
  • LOC105322156 (NCBI:GeneID:105322156): nuclear RNA export factor 1 (log2FC=0.44; adjusted p=4.2e-11)
  • LOC105324926 (NCBI:GeneID:105324926): bifunctional peptidase and arginyl-hydroxylase JMJD5 (log2FC=1.03; adjusted p=4.27e-11)
  • LOC117686524 (NCBI:GeneID:117686524): angiotensin-converting enzyme (log2FC=1.12; adjusted p=6.7e-11)
  • LOC105326440 (NCBI:GeneID:105326440): homeobox protein Hox-B5a (log2FC=0.67; adjusted p=7.24e-11)

Acidified Lower Fdr Lt 0.05

Genes: 1,990; RefSeq-characterized descriptions: 1,129 (56.7%).

  • LOC105326150 (NCBI:GeneID:105326150): hillarin (log2FC=-0.78; adjusted p=1.57e-12)
  • LOC109619691 (NCBI:GeneID:109619691): filamin-A (log2FC=-0.64; adjusted p=3.32e-11)
  • LOC136273810 (NCBI:GeneID:136273810): N66 matrix protein-like (log2FC=-6.68; adjusted p=2.72e-10)
  • LOC105345458 (NCBI:GeneID:105345458): cytochrome P450 3A9 (log2FC=-3.39; adjusted p=6.05e-10)
  • LOC105328706 (NCBI:GeneID:105328706): parathyroid hormone 2 receptor (log2FC=-2.58; adjusted p=1.1e-09)
  • LOC105327137 (NCBI:GeneID:105327137): collagen alpha-5(VI) chain (log2FC=-0.55; adjusted p=2.16e-08)
  • LOC136273184 (NCBI:GeneID:136273184): A disintegrin and metalloproteinase with thrombospondin motifs 17-like (log2FC=-1.58; adjusted p=5.8e-08)
  • LOC105341580 (NCBI:GeneID:105341580): toll-like receptor 3 (log2FC=-0.89; adjusted p=6.15e-08)
  • LOC117682434 (NCBI:GeneID:117682434): LHFPL tetraspan subfamily member 3 protein (log2FC=-0.84; adjusted p=2.1e-07)
  • LOC105334418 (NCBI:GeneID:105334418): mitogen-activated protein kinase 1 (log2FC=-0.24; adjusted p=3.54e-07)
  • LOC105330360 (NCBI:GeneID:105330360): parathyroid hormone/parathyroid hormone-related peptide receptor (log2FC=-2.13; adjusted p=3.72e-07)
  • LOC105335536 (NCBI:GeneID:105335536): cyclin-O (log2FC=-2.63; adjusted p=3.94e-07)
  • LOC105320161 (NCBI:GeneID:105320161): arginine kinase (log2FC=-0.73; adjusted p=4.09e-07)
  • LOC105347438 (NCBI:GeneID:105347438): neutral ceramidase B (log2FC=-0.61; adjusted p=4.4e-07)
  • LOC105323283 (NCBI:GeneID:105323283): toll-like receptor 4 (log2FC=-1.47; adjusted p=5.53e-07)

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: protein_coding (2480 observed, 2321.0 expected; fold=1.07; adjusted p=2.89e-20)
  • acidified lower fdr lt 0.05: protein_coding (1775 observed, 1688.8 expected; fold=1.05; adjusted p=1.85e-08)

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.