PRJNA756710 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.

Low Salinity Higher Fdr Lt 0.05

Genes: 1,825; RefSeq-characterized descriptions: 1,240 (67.9%).

  • LOC105321584 (NCBI:GeneID:105321584): cysteine sulfinic acid decarboxylase (log2FC=8.53; adjusted p=1.3e-84)
  • LOC105334814 (NCBI:GeneID:105334814): baculoviral IAP repeat-containing protein 2 (log2FC=4.68; adjusted p=9.38e-49)
  • LOC105317679 (NCBI:GeneID:105317679): carnosine synthase 1 (log2FC=7.59; adjusted p=5.36e-46)
  • LOC105329513 (NCBI:GeneID:105329513): dual specificity protein phosphatase 10 (log2FC=3.14; adjusted p=4.16e-36)
  • LOC105325560 (NCBI:GeneID:105325560): class E basic helix-loop-helix protein 40 (log2FC=2.26; adjusted p=3.05e-22)
  • LOC105324933 (NCBI:GeneID:105324933): platelet-activating factor acetylhydrolase (log2FC=3.50; adjusted p=6.57e-21)
  • LOC105332789 (NCBI:GeneID:105332789): cytochrome P450 26A1 (log2FC=3.18; adjusted p=8.74e-20)
  • LOC105323642 (NCBI:GeneID:105323642): immediate early response gene 5-like protein (log2FC=1.72; adjusted p=2.49e-18)
  • LOC105337679 (NCBI:GeneID:105337679): sodium- and chloride-dependent glycine transporter 1-like (log2FC=3.51; adjusted p=6.59e-18)
  • LOC105318660 (NCBI:GeneID:105318660): multidrug resistance-associated protein 1 (log2FC=6.69; adjusted p=3.29e-17)
  • LOC105318134 (NCBI:GeneID:105318134): zinc finger CCCH domain-containing protein 13 (log2FC=3.37; adjusted p=3.99e-17)
  • LOC105318659 (NCBI:GeneID:105318659): multidrug resistance-associated protein 1 (log2FC=6.14; adjusted p=8.08e-17)
  • LOC105336262 (NCBI:GeneID:105336262): beta-1,3-galactosyltransferase 1 (log2FC=1.98; adjusted p=6.23e-16)
  • LOC105331566 (NCBI:GeneID:105331566): transcription factor MafK (log2FC=2.45; adjusted p=8.33e-16)
  • LOC105337716 (NCBI:GeneID:105337716): basic leucine zipper transcriptional factor ATF-like (log2FC=3.57; adjusted p=2.32e-15)

Low Salinity Lower Fdr Lt 0.05

Genes: 1,220; RefSeq-characterized descriptions: 906 (74.3%).

  • LOC136275614 (NCBI:GeneID:136275614): deleted in malignant brain tumors 1 protein-like (log2FC=-2.05; adjusted p=8.29e-11)
  • LOC136276552 (NCBI:GeneID:136276552): nesprin-1-like (log2FC=-1.40; adjusted p=8.36e-11)
  • LOC105329810 (NCBI:GeneID:105329810): synaptobrevin-A (log2FC=-2.05; adjusted p=1.57e-10)
  • LOC109618951 (NCBI:GeneID:109618951): vesicle-associated membrane protein 3-like (log2FC=-2.62; adjusted p=1.68e-10)
  • LOC105318047 (NCBI:GeneID:105318047): zinc finger protein 384 (log2FC=-1.23; adjusted p=7.67e-10)
  • LOC105328381 (NCBI:GeneID:105328381): transmembrane protein 45B (log2FC=-1.78; adjusted p=2.76e-09)
  • LOC105336388 (NCBI:GeneID:105336388): RNA-binding protein Ro60 (log2FC=-1.34; adjusted p=5.04e-09)
  • LOC105332083 (NCBI:GeneID:105332083): zinc finger protein 616 (log2FC=-1.71; adjusted p=5.04e-09)
  • LOC105342063 (NCBI:GeneID:105342063): ATPase family AAA domain-containing protein 2 (log2FC=-0.95; adjusted p=5.74e-09)
  • LOC105320721 (NCBI:GeneID:105320721): tubulin–tyrosine ligase-like protein 12 (log2FC=-1.39; adjusted p=1.61e-08)
  • LOC105336382 (NCBI:GeneID:105336382): outer dense fiber protein 2 (log2FC=-1.15; adjusted p=2.54e-08)
  • LOC105342516 (NCBI:GeneID:105342516): serine-rich adhesin for platelets (log2FC=-1.73; adjusted p=4.01e-08)
  • LOC105327465 (NCBI:GeneID:105327465): hamartin (log2FC=-1.46; adjusted p=5.86e-08)
  • LOC105323732 (NCBI:GeneID:105323732): apoptosis-inducing factor 3 (log2FC=-1.26; adjusted p=6.8e-08)
  • LOC105324626 (NCBI:GeneID:105324626): protocadherin Fat 4 (log2FC=-1.41; adjusted p=9.15e-08)

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.

  • low salinity higher fdr lt 0.05: protein_coding (1691 observed, 1635.1 expected; fold=1.03; adjusted p=7.23e-06)
  • low salinity higher fdr lt 0.05: rRNA (10 observed, 0.8 expected; fold=11.77; adjusted p=1.15e-10)
  • low salinity lower fdr lt 0.05: protein_coding (1165 observed, 1093.0 expected; fold=1.07; adjusted p=1.48e-13)

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.