PRJNA515169 (vcrassostreae_J2_9) 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.

Vcrassostreae J2 9 Higher Fdr Lt 0.05

Genes: 453; RefSeq-characterized descriptions: 317 (70.0%).

  • LOC105321376 (NCBI:GeneID:105321376): EF-hand calcium-binding domain-containing protein 1 (log2FC=3.50; adjusted p=2.73e-141)
  • LOC136273704 (NCBI:GeneID:136273704): coadhesin-like (log2FC=3.25; adjusted p=1.28e-91)
  • LOC136273062 (NCBI:GeneID:136273062): galanin receptor 2b-like (log2FC=2.33; adjusted p=1.6e-60)
  • LOC105342241 (NCBI:GeneID:105342241): hypothetical protein (log2FC=4.64; adjusted p=5.23e-53)
  • LOC105318026 (NCBI:GeneID:105318026): tumor necrosis factor receptor superfamily member 11A (log2FC=2.93; adjusted p=1.45e-52)
  • LOC105322542 (NCBI:GeneID:105322542): interleukin 17-like protein (log2FC=3.94; adjusted p=4.99e-41)
  • LOC105321692 (NCBI:GeneID:105321692): cytochrome P450 2C31-like (log2FC=2.47; adjusted p=1.07e-39)
  • LOC105320131 (NCBI:GeneID:105320131): prostaglandin E2 receptor EP4 subtype (log2FC=2.41; adjusted p=6.18e-39)
  • LOC105329610 (NCBI:GeneID:105329610): FMRFamide receptor (log2FC=2.20; adjusted p=2.98e-35)
  • LOC105325106 (NCBI:GeneID:105325106): G-protein coupled receptor dmsr-1 (log2FC=2.18; adjusted p=4.13e-27)
  • LOC105344708 (NCBI:GeneID:105344708): deleted in malignant brain tumors 1 protein (log2FC=1.49; adjusted p=9.58e-25)
  • LOC136273331 (NCBI:GeneID:136273331): scavenger receptor class A member 5-like (log2FC=3.19; adjusted p=1.78e-24)
  • LOC105325515 (NCBI:GeneID:105325515): transcription factor ETV7 (log2FC=1.64; adjusted p=1.66e-23)
  • LOC105347308 (NCBI:GeneID:105347308): myeloid differentiation primary response protein MyD88 (log2FC=1.67; adjusted p=8.18e-23)
  • LOC105325829 (NCBI:GeneID:105325829): vesicular glutamate transporter 2.2 (log2FC=2.20; adjusted p=2.83e-20)

Vcrassostreae J2 9 Lower Fdr Lt 0.05

Genes: 106; RefSeq-characterized descriptions: 64 (60.4%).

  • LOC117682859 (NCBI:GeneID:117682859): alpha-2 adrenergic receptor (log2FC=-1.51; adjusted p=5.86e-16)
  • LOC105324307 (NCBI:GeneID:105324307): frizzled-7-A (log2FC=-1.35; adjusted p=9.25e-13)
  • LOC105322271 (NCBI:GeneID:105322271): transforming growth factor-beta-induced protein ig-h3 (log2FC=-1.00; adjusted p=1.57e-12)
  • LOC105322874 (NCBI:GeneID:105322874): low affinity immunoglobulin epsilon Fc receptor (log2FC=-1.24; adjusted p=6.86e-08)
  • LOC105341060 (NCBI:GeneID:105341060): integrin beta-1 (log2FC=-0.85; adjusted p=2.78e-07)
  • LOC105344734 (NCBI:GeneID:105344734): low-density lipoprotein receptor-related protein 4 (log2FC=-0.94; adjusted p=3.89e-07)
  • LOC105348479 (NCBI:GeneID:105348479): low-density lipoprotein receptor (log2FC=-0.96; adjusted p=7.93e-07)
  • LOC105344630 (NCBI:GeneID:105344630): endothelin-converting enzyme 1 (log2FC=-0.96; adjusted p=2.57e-06)
  • LOC105340170 (NCBI:GeneID:105340170): stabilin-2 (log2FC=-0.91; adjusted p=6.95e-06)
  • LOC105341917 (NCBI:GeneID:105341917): transient receptor potential cation channel subfamily M member-like 2 (log2FC=-1.04; adjusted p=8.16e-06)
  • LOC105341812 (NCBI:GeneID:105341812): aquaporin-1 (log2FC=-0.97; adjusted p=9.21e-06)
  • LOC136275826 (NCBI:GeneID:136275826): myosin heavy chain, clone 203-like (log2FC=-0.88; adjusted p=1.69e-05)
  • LOC117688786 (NCBI:GeneID:117688786): antifreeze protein Maxi-like (log2FC=-1.41; adjusted p=1.72e-05)
  • LOC105322476 (NCBI:GeneID:105322476): macrophage mannose receptor 1 (log2FC=-0.80; adjusted p=2.72e-05)
  • LOC117688268 (NCBI:GeneID:117688268): NADPH oxidase 5 (log2FC=-0.95; adjusted p=0.000162)

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.

  • vcrassostreae J2 9 higher fdr lt 0.05: protein_coding (432 observed, 402.8 expected; fold=1.07; adjusted p=4.83e-06)
  • vcrassostreae J2 9 lower fdr lt 0.05: rRNA (10 observed, 0.1 expected; fold=151.79; adjusted p=6.11e-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.