PRJNA694496 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.

Selected Higher Fdr Lt 0.05

Genes: 4,353; RefSeq-characterized descriptions: 2,703 (62.1%).

  • LOC105340999 (NCBI:GeneID:105340999): A disintegrin and metalloproteinase with thrombospondin motifs adt-1 (log2FC=5.91; adjusted p=2.6e-90)
  • LOC105348543 (NCBI:GeneID:105348543): perilipin-2 (log2FC=2.08; adjusted p=8.47e-77)
  • LOC136270966 (NCBI:GeneID:136270966): coadhesin-like (log2FC=4.43; adjusted p=3.45e-67)
  • LOC105332528 (NCBI:GeneID:105332528): baculoviral IAP repeat-containing protein 8 (log2FC=2.20; adjusted p=1.82e-54)
  • LOC105324352 (NCBI:GeneID:105324352): natterin-3 (log2FC=5.41; adjusted p=1.13e-53)
  • LOC136273127 (NCBI:GeneID:136273127): sterile alpha motif domain-containing protein 9-like (log2FC=1.65; adjusted p=8.75e-49)
  • LOC105321969 (NCBI:GeneID:105321969): temptin (log2FC=4.35; adjusted p=4.19e-46)
  • LOC105328968 (NCBI:GeneID:105328968): F-box only protein 4 (log2FC=1.90; adjusted p=1.09e-45)
  • LOC105348808 (NCBI:GeneID:105348808): coadhesin (log2FC=1.67; adjusted p=3.24e-42)
  • LOC105343805 (NCBI:GeneID:105343805): interferon regulatory factor 2 (log2FC=2.52; adjusted p=2.75e-40)
  • LOC105347149 (NCBI:GeneID:105347149): NAD-dependent protein deacetylase Sirt6 (log2FC=1.82; adjusted p=1.48e-38)
  • LOC105335677 (NCBI:GeneID:105335677): histone acetyltransferase p300 (log2FC=2.82; adjusted p=2.4e-36)
  • LOC136269516 (NCBI:GeneID:136269516): sacsin-like (log2FC=3.54; adjusted p=9.44e-36)
  • LOC105343686 (NCBI:GeneID:105343686): ubiquitin carboxyl-terminal hydrolase 46 (log2FC=3.62; adjusted p=4.53e-34)
  • LOC105337198 (NCBI:GeneID:105337198): fibrocystin-L (log2FC=2.71; adjusted p=1.24e-33)

Selected Lower Fdr Lt 0.05

Genes: 4,449; RefSeq-characterized descriptions: 3,271 (73.5%).

  • LOC117686572 (NCBI:GeneID:117686572): sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1 (log2FC=-5.92; adjusted p=4.56e-215)
  • LOC117681484 (NCBI:GeneID:117681484): transforming growth factor-beta-induced protein ig-h3-like (log2FC=-4.29; adjusted p=5.48e-108)
  • LOC105318991 (NCBI:GeneID:105318991): sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1 (log2FC=-3.39; adjusted p=3.3e-97)
  • LOC117686571 (NCBI:GeneID:117686571): sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1 (log2FC=-4.95; adjusted p=5.49e-94)
  • LOC105323084 (NCBI:GeneID:105323084): SCO-spondin (log2FC=-3.00; adjusted p=7.63e-86)
  • LOC105344090 (NCBI:GeneID:105344090): mesenchyme-specific cell surface glycoprotein (log2FC=-4.97; adjusted p=4.47e-82)
  • LOC105342460 (NCBI:GeneID:105342460): tenascin (log2FC=-3.29; adjusted p=4.44e-73)
  • LOC105341033 (NCBI:GeneID:105341033): collagen alpha-1(XIV) chain (log2FC=-2.10; adjusted p=3.88e-68)
  • LOC105339449 (NCBI:GeneID:105339449): geranylgeranyl transferase type-1 subunit beta (log2FC=-2.31; adjusted p=1.12e-67)
  • LOC105318009 (NCBI:GeneID:105318009): Golgi-associated plant pathogenesis-related protein 1 (log2FC=-3.20; adjusted p=7.3e-67)
  • LOC136271471 (NCBI:GeneID:136271471): transforming growth factor-beta-induced protein ig-h3-like (log2FC=-2.22; adjusted p=2.61e-66)
  • LOC105343145 (NCBI:GeneID:105343145): apolipoprotein D (log2FC=-3.12; adjusted p=2.81e-64)
  • LOC105322971 (NCBI:GeneID:105322971): transcription factor atf-2 (log2FC=-2.13; adjusted p=1.06e-63)
  • LOC109619724 (NCBI:GeneID:109619724): endoglucanase (log2FC=-2.74; adjusted p=1.17e-63)
  • LOC105340827 (NCBI:GeneID:105340827): heme-binding protein 2 (log2FC=-4.09; adjusted p=1.42e-61)

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.

  • selected higher fdr lt 0.05: lncRNA (362 observed, 283.8 expected; fold=1.28; adjusted p=2.89e-07)
  • selected higher fdr lt 0.05: rRNA (15 observed, 3.3 expected; fold=4.55; adjusted p=7.88e-10)
  • selected lower fdr lt 0.05: protein_coding (4265 observed, 4129.5 expected; fold=1.03; adjusted p=2.65e-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.