PRJNA515169 (vtasmaniensis_LGP32) 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.

Vtasmaniensis Lgp32 Higher Fdr Lt 0.05

Genes: 397; RefSeq-characterized descriptions: 280 (70.5%).

  • LOC105321376 (NCBI:GeneID:105321376): EF-hand calcium-binding domain-containing protein 1 (log2FC=3.49; adjusted p=5.86e-173)
  • LOC136273704 (NCBI:GeneID:136273704): coadhesin-like (log2FC=3.10; adjusted p=4.39e-80)
  • LOC105342241 (NCBI:GeneID:105342241): hypothetical protein (log2FC=4.69; adjusted p=1.38e-55)
  • LOC136273062 (NCBI:GeneID:136273062): galanin receptor 2b-like (log2FC=2.19; adjusted p=4.05e-50)
  • LOC105318026 (NCBI:GeneID:105318026): tumor necrosis factor receptor superfamily member 11A (log2FC=2.74; adjusted p=4.61e-48)
  • LOC105321692 (NCBI:GeneID:105321692): cytochrome P450 2C31-like (log2FC=2.50; adjusted p=1.11e-42)
  • LOC105332146 (NCBI:GeneID:105332146): serum amyloid A-5 protein (log2FC=2.63; adjusted p=3.88e-40)
  • LOC105320131 (NCBI:GeneID:105320131): prostaglandin E2 receptor EP4 subtype (log2FC=2.45; adjusted p=1.43e-39)
  • LOC105329610 (NCBI:GeneID:105329610): FMRFamide receptor (log2FC=2.18; adjusted p=4.42e-38)
  • LOC105325106 (NCBI:GeneID:105325106): G-protein coupled receptor dmsr-1 (log2FC=2.24; adjusted p=2.08e-29)
  • LOC105322542 (NCBI:GeneID:105322542): interleukin 17-like protein (log2FC=3.42; adjusted p=1.66e-24)
  • LOC105325829 (NCBI:GeneID:105325829): vesicular glutamate transporter 2.2 (log2FC=2.31; adjusted p=1.33e-23)
  • LOC105317911 (NCBI:GeneID:105317911): proton-coupled zinc antiporter SLC30A1 (log2FC=1.37; adjusted p=5.01e-23)
  • LOC136273331 (NCBI:GeneID:136273331): scavenger receptor class A member 5-like (log2FC=3.19; adjusted p=2.47e-20)
  • LOC105321152 (NCBI:GeneID:105321152): inter-alpha-trypsin inhibitor heavy chain H4 (log2FC=1.14; adjusted p=1.5e-19)

Vtasmaniensis Lgp32 Lower Fdr Lt 0.05

Genes: 92; RefSeq-characterized descriptions: 62 (67.4%).

  • LOC117682859 (NCBI:GeneID:117682859): alpha-2 adrenergic receptor (log2FC=-1.44; adjusted p=4.93e-14)
  • LOC105324307 (NCBI:GeneID:105324307): frizzled-7-A (log2FC=-1.34; adjusted p=3.92e-13)
  • LOC105322271 (NCBI:GeneID:105322271): transforming growth factor-beta-induced protein ig-h3 (log2FC=-0.91; adjusted p=2.73e-10)
  • LOC105322874 (NCBI:GeneID:105322874): low affinity immunoglobulin epsilon Fc receptor (log2FC=-1.31; adjusted p=1.39e-07)
  • LOC105339801 (NCBI:GeneID:105339801): zinc transporter ZIP10 (log2FC=-0.89; adjusted p=6.47e-07)
  • LOC105348479 (NCBI:GeneID:105348479): low-density lipoprotein receptor (log2FC=-0.80; adjusted p=9.63e-07)
  • LOC105341060 (NCBI:GeneID:105341060): integrin beta-1 (log2FC=-0.83; adjusted p=9.63e-07)
  • LOC105341917 (NCBI:GeneID:105341917): transient receptor potential cation channel subfamily M member-like 2 (log2FC=-1.19; adjusted p=9.89e-07)
  • LOC117688268 (NCBI:GeneID:117688268): NADPH oxidase 5 (log2FC=-1.14; adjusted p=1.83e-06)
  • LOC105341812 (NCBI:GeneID:105341812): aquaporin-1 (log2FC=-0.98; adjusted p=1.31e-05)
  • LOC105340170 (NCBI:GeneID:105340170): stabilin-2 (log2FC=-0.88; adjusted p=2.49e-05)
  • LOC105346342 (NCBI:GeneID:105346342): retinoid-inducible serine carboxypeptidase (log2FC=-1.01; adjusted p=2.82e-05)
  • LOC105322476 (NCBI:GeneID:105322476): macrophage mannose receptor 1 (log2FC=-0.79; adjusted p=3.22e-05)
  • LOC105344734 (NCBI:GeneID:105344734): low-density lipoprotein receptor-related protein 4 (log2FC=-0.87; adjusted p=3.38e-05)
  • LOC136275826 (NCBI:GeneID:136275826): myosin heavy chain, clone 203-like (log2FC=-0.89; adjusted p=3.58e-05)

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.

  • vtasmaniensis LGP32 higher fdr lt 0.05: protein_coding (379 observed, 353.5 expected; fold=1.07; adjusted p=1.81e-05)
  • vtasmaniensis LGP32 lower fdr lt 0.05: rRNA (10 observed, 0.1 expected; fold=173.80; adjusted p=1.23e-20)

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.