PRJEB58194 (f0_exposed) 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.

F0 Exposed Higher Fdr Lt 0.05

Genes: 255; RefSeq-characterized descriptions: 197 (77.3%).

LOC117684588 (NCBI:GeneID:117684588): forkhead box protein J3 (log2FC=1.42; adjusted p=3.4e-07)
LOC105344432 (NCBI:GeneID:105344432): M-phase inducer phosphatase (log2FC=1.90; adjusted p=7.11e-06)
LOC105325413 (NCBI:GeneID:105325413): mitochondrial enolase superfamily member 1 (log2FC=0.41; adjusted p=8.39e-05)
LOC105319369 (NCBI:GeneID:105319369): protein moonraker (log2FC=0.31; adjusted p=0.000167)
LOC105344440 (NCBI:GeneID:105344440): M-phase inducer phosphatase (log2FC=1.51; adjusted p=0.000253)
LOC105348733 (NCBI:GeneID:105348733): G2/mitotic-specific cyclin-A (log2FC=0.51; adjusted p=0.000273)
LOC105347029 (NCBI:GeneID:105347029): carboxy-terminal kinesin 2 (log2FC=0.35; adjusted p=0.000324)
LOC105318098 (NCBI:GeneID:105318098): polyhomeotic-like protein 2 (log2FC=0.31; adjusted p=0.000431)
LOC105317663 (NCBI:GeneID:105317663): nucleoside hydrolase (log2FC=0.67; adjusted p=0.000431)
LOC105343283 (NCBI:GeneID:105343283): titin (log2FC=1.26; adjusted p=0.000519)
LOC105342289 (NCBI:GeneID:105342289): ETS-related transcription factor Elf-3 (log2FC=1.13; adjusted p=0.000663)
LOC105344441 (NCBI:GeneID:105344441): M-phase inducer phosphatase 1-like (log2FC=1.90; adjusted p=0.000881)
LOC105320581 (NCBI:GeneID:105320581): MAM and LDL-receptor class A domain-containing protein 2 (log2FC=0.50; adjusted p=0.000933)
LOC105318173 (NCBI:GeneID:105318173): beta-mannosidase (log2FC=0.55; adjusted p=0.000945)
LOC105331365 (NCBI:GeneID:105331365): HAUS augmin-like complex subunit 4 (log2FC=0.41; adjusted p=0.00135)

F0 Exposed Lower Fdr Lt 0.05

Genes: 389; RefSeq-characterized descriptions: 248 (63.8%).

LOC136270632 (NCBI:GeneID:136270632): cytochrome P450 2C14-like (log2FC=-2.34; adjusted p=3.4e-07)
LOC105318673 (NCBI:GeneID:105318673): hypothetical protein (log2FC=-1.73; adjusted p=4.68e-07)
LOC136270694 (NCBI:GeneID:136270694): eggshell protein-like (log2FC=-2.10; adjusted p=2.53e-05)
LOC105318858 (NCBI:GeneID:105318858): homeobox protein engrailed-1-B (log2FC=-1.41; adjusted p=4.4e-05)
LOC105319984 (NCBI:GeneID:105319984): low-density lipoprotein receptor-related protein 12 (log2FC=-1.61; adjusted p=5.84e-05)
LOC105338625 (NCBI:GeneID:105338625): fatty acid 2-hydroxylase (log2FC=-1.17; adjusted p=5.84e-05)
LOC105324613 (NCBI:GeneID:105324613): chitin synthase chs-2 (log2FC=-0.61; adjusted p=0.000167)
LOC105326564 (NCBI:GeneID:105326564): peroxisomal membrane protein PEX13 (log2FC=-2.41; adjusted p=0.000185)
LOC105333607 (NCBI:GeneID:105333607): protein white (log2FC=-1.89; adjusted p=0.00021)
LOC105326742 (NCBI:GeneID:105326742): glycoprotein 3-alpha-L-fucosyltransferase A (log2FC=-0.90; adjusted p=0.000253)
LOC105345532 (NCBI:GeneID:105345532): integrin alpha-8 (log2FC=-1.09; adjusted p=0.000277)
LOC105333627 (NCBI:GeneID:105333627): tetraspanin-9 (log2FC=-0.72; adjusted p=0.000277)
LOC105341424 (NCBI:GeneID:105341424): fatty acid-binding protein, intestinal (log2FC=-3.06; adjusted p=0.000331)
LOC105329522 (NCBI:GeneID:105329522): transcriptional-regulating factor 1 (log2FC=-1.00; adjusted p=0.000331)
LOC105348415 (NCBI:GeneID:105348415): steroid 17-alpha-hydroxylase/17,20 lyase-like (log2FC=-2.32; adjusted p=0.000362)

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.

f0 exposed higher fdr lt 0.05: protein_coding (249 observed, 230.1 expected; fold=1.08; adjusted p=3.96e-05)
f0 exposed lower fdr lt 0.05: lncRNA (53 observed, 35.2 expected; fold=1.51; adjusted p=0.012)

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.