PRJNA407831 (h24) 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.

H24 Higher Fdr Lt 0.05

Genes: 1,363; RefSeq-characterized descriptions: 1,059 (77.7%).

  • LOC117690579 (NCBI:GeneID:117690579): small nucleolar RNA U3 (log2FC=6.18; adjusted p=9.36e-36)
  • LOC105348305 (NCBI:GeneID:105348305): heat shock protein 68-like (log2FC=7.59; adjusted p=1.37e-33)
  • LOC105334510 (NCBI:GeneID:105334510): heat shock protein 68-like (log2FC=7.57; adjusted p=5.58e-29)
  • LOC105334580 (NCBI:GeneID:105334580): BAG family molecular chaperone regulator 3 (log2FC=5.62; adjusted p=1.28e-27)
  • LOC105331925 (NCBI:GeneID:105331925): serine/threonine-protein kinase PRP4 homolog (log2FC=0.69; adjusted p=1.34e-27)
  • LOC105345482 (NCBI:GeneID:105345482): BUB3-interacting and GLEBS motif-containing protein ZNF207 (log2FC=0.43; adjusted p=5.98e-26)
  • LOC105340538 (NCBI:GeneID:105340538): protein hook homolog (log2FC=1.42; adjusted p=1.34e-23)
  • LOC105329483 (NCBI:GeneID:105329483): tolloid-like protein 1 (log2FC=0.43; adjusted p=2.54e-17)
  • LOC117691913 (NCBI:GeneID:117691913): alpha-crystallin A chain-like (log2FC=6.51; adjusted p=2.22e-16)
  • LOC105323147 (NCBI:GeneID:105323147): RNA-binding protein 26 (log2FC=0.54; adjusted p=3.72e-15)
  • LOC105343216 (NCBI:GeneID:105343216): heat shock protein Hsp-16.48/Hsp-16.49 (log2FC=6.68; adjusted p=1.45e-14)
  • LOC105329159 (NCBI:GeneID:105329159): hypothetical protein (log2FC=2.79; adjusted p=1.59e-13)
  • LOC105325416 (NCBI:GeneID:105325416): inactive rhomboid protein 2 (log2FC=0.81; adjusted p=2.25e-13)
  • LOC105347203 (NCBI:GeneID:105347203): SPARC (log2FC=0.67; adjusted p=2.9e-13)
  • LOC105341339 (NCBI:GeneID:105341339): CREB/ATF bZIP transcription factor (log2FC=0.71; adjusted p=2.31e-12)

H24 Lower Fdr Lt 0.05

Genes: 1,351; RefSeq-characterized descriptions: 958 (70.9%).

  • LOC105318591 (NCBI:GeneID:105318591): serine/threonine-protein kinase TBK1 (log2FC=-1.38; adjusted p=1.44e-53)
  • LOC105346591 (NCBI:GeneID:105346591): kelch-like protein 18 (log2FC=-0.89; adjusted p=2.31e-37)
  • LOC105321326 (NCBI:GeneID:105321326): endoplasmic reticulum membrane sensor NFE2L1 (log2FC=-2.46; adjusted p=1.58e-30)
  • LOC105322996 (NCBI:GeneID:105322996): nuclear protein AMMECR1 (log2FC=-4.03; adjusted p=3.92e-27)
  • LOC105344547 (NCBI:GeneID:105344547): F-box and WD repeat domain-containing 11-B (log2FC=-1.54; adjusted p=4.95e-23)
  • LOC105348719 (NCBI:GeneID:105348719): protein PTHB1 (log2FC=-0.54; adjusted p=1.64e-19)
  • LOC105330037 (NCBI:GeneID:105330037): ATP-dependent RNA helicase me31b (log2FC=-0.70; adjusted p=4.41e-18)
  • LOC105344453 (NCBI:GeneID:105344453): band 4.1-like protein 1 (log2FC=-0.41; adjusted p=7.25e-18)
  • LOC105324775 (NCBI:GeneID:105324775): RNA-binding protein 24-A (log2FC=-0.62; adjusted p=1.02e-17)
  • LOC105337075 (NCBI:GeneID:105337075): arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2 (log2FC=-0.41; adjusted p=1.38e-17)
  • LOC105336547 (NCBI:GeneID:105336547): endothelin-converting enzyme homolog (log2FC=-0.69; adjusted p=4.33e-16)
  • LOC105322510 (NCBI:GeneID:105322510): innexin unc-9 (log2FC=-0.35; adjusted p=1.88e-14)
  • LOC105332231 (NCBI:GeneID:105332231): myocyte-specific enhancer factor 2C (log2FC=-0.35; adjusted p=1.45e-12)
  • LOC117684612 (NCBI:GeneID:117684612): serine/threonine-protein kinase NIM1 (log2FC=-0.61; adjusted p=2.31e-12)
  • LOC105335111 (NCBI:GeneID:105335111): single-stranded DNA-binding protein 2 (log2FC=-0.24; adjusted p=3.01e-12)

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.

  • h24 higher fdr lt 0.05: protein_coding (1268 observed, 1210.7 expected; fold=1.05; adjusted p=3.35e-07)
  • h24 higher fdr lt 0.05: snRNA (2 observed, 0.1 expected; fold=17.08; adjusted p=0.016)
  • h24 lower fdr lt 0.05: protein_coding (1300 observed, 1200.0 expected; fold=1.08; adjusted p=8.46e-23)

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.