PRJNA1329250 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.

Oshv1 Uvar Higher Fdr Lt 0.05

Genes: 3,237; RefSeq-characterized descriptions: 2,079 (64.2%).

  • LOC136276189 (NCBI:GeneID:136276189): NFX1-type zinc finger-containing protein 1-like (log2FC=2.34; adjusted p=6.71e-30)
  • LOC105343525 (NCBI:GeneID:105343525): myb-like protein X (log2FC=3.16; adjusted p=1.93e-28)
  • LOC105336469 (NCBI:GeneID:105336469): NFX1-type zinc finger-containing protein 1 (log2FC=2.55; adjusted p=3.41e-25)
  • LOC105345480 (NCBI:GeneID:105345480): probable ATP-dependent RNA helicase DDX46 (log2FC=3.10; adjusted p=1.18e-20)
  • LOC136270275 (NCBI:GeneID:136270275): 3’-5’ exoribonuclease HELZ2-like (log2FC=2.85; adjusted p=3.48e-20)
  • LOC109618139 (NCBI:GeneID:109618139): sacsin (log2FC=2.32; adjusted p=1.14e-19)
  • LOC117684474 (NCBI:GeneID:117684474): NFX1-type zinc finger-containing protein 1 (log2FC=3.19; adjusted p=1.77e-19)
  • LOC105342383 (NCBI:GeneID:105342383): rhamnose-binding lectin (log2FC=3.33; adjusted p=1.77e-19)
  • LOC105319712 (NCBI:GeneID:105319712): interferon-induced helicase C domain-containing protein 1 (log2FC=2.68; adjusted p=2.45e-19)
  • LOC105343686 (NCBI:GeneID:105343686): ubiquitin carboxyl-terminal hydrolase 46 (log2FC=3.40; adjusted p=3.23e-19)
  • LOC105341799 (NCBI:GeneID:105341799): ATP-dependent RNA helicase DHX58 (log2FC=2.00; adjusted p=3.23e-19)
  • LOC105334103 (NCBI:GeneID:105334103): ubiquitin carboxyl-terminal hydrolase 2 (log2FC=2.79; adjusted p=5.83e-19)
  • LOC105324401 (NCBI:GeneID:105324401): probable E3 ubiquitin-protein ligase RNF144A (log2FC=3.07; adjusted p=9.35e-19)
  • LOC105340146 (NCBI:GeneID:105340146): 3’-5’ exoribonuclease HELZ2 (log2FC=2.56; adjusted p=1.32e-18)
  • LOC105325677 (NCBI:GeneID:105325677): proprotein convertase subtilisin/kexin type 5 (log2FC=2.34; adjusted p=1.32e-18)

Oshv1 Uvar Lower Fdr Lt 0.05

Genes: 2,209; RefSeq-characterized descriptions: 1,579 (71.5%).

  • LOC105346802 (NCBI:GeneID:105346802): carbonic anhydrase (log2FC=-1.23; adjusted p=4.5e-08)
  • LOC105341997 (NCBI:GeneID:105341997): ankyrin repeat domain-containing protein 50 (log2FC=-0.62; adjusted p=1.59e-07)
  • LOC105320087 (NCBI:GeneID:105320087): ankyrin-1 (log2FC=-0.83; adjusted p=1.87e-07)
  • LOC105347274 (NCBI:GeneID:105347274): leucine-rich repeat-containing protein 74B (log2FC=-0.73; adjusted p=5.39e-07)
  • LOC105344389 (NCBI:GeneID:105344389): aldehyde dehydrogenase, mitochondrial (log2FC=-0.49; adjusted p=9.3e-07)
  • LOC105347466 (NCBI:GeneID:105347466): IQ motif and ankyrin repeat domain-containing protein 1 (log2FC=-0.42; adjusted p=9.5e-07)
  • LOC105323009 (NCBI:GeneID:105323009): cleavage stimulation factor subunit 1 (log2FC=-0.38; adjusted p=1.09e-06)
  • LOC109619061 (NCBI:GeneID:109619061): arrestin domain-containing protein 3 (log2FC=-0.41; adjusted p=1.21e-06)
  • LOC105321140 (NCBI:GeneID:105321140): molybdate-anion transporter (log2FC=-0.24; adjusted p=1.39e-06)
  • LOC105325607 (NCBI:GeneID:105325607): WD repeat-containing protein 5B (log2FC=-0.47; adjusted p=1.98e-06)
  • LOC105319099 (NCBI:GeneID:105319099): serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit A (log2FC=-0.84; adjusted p=2.22e-06)
  • LOC105337965 (NCBI:GeneID:105337965): E3 ubiquitin-protein ligase TRIM56-like (log2FC=-0.82; adjusted p=2.99e-06)
  • LOC105339423 (NCBI:GeneID:105339423): pyridoxine-5’-phosphate oxidase (log2FC=-0.57; adjusted p=3.54e-06)
  • LOC105323743 (NCBI:GeneID:105323743): arylsulfatase B (log2FC=-0.97; adjusted p=4.51e-06)
  • LOC105333343 (NCBI:GeneID:105333343): protein inturned (log2FC=-0.60; adjusted p=5.98e-06)

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.

  • oshv1 uvar higher fdr lt 0.05: protein_coding (2962 observed, 2765.2 expected; fold=1.07; adjusted p=7.94e-28)
  • oshv1 uvar lower fdr lt 0.05: protein_coding (2124 observed, 1887.0 expected; fold=1.13; adjusted p=1.59e-64)

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.