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. 2022 Mar 21;7(2):e01290-21. doi: 10.1128/msystems.01290-21

TABLE 2.

Significantly enriched Gene Ontology terms in the critical genes in the lettuce leaf subset

GO identifier GO term Total no. of genesa No. of genes in subsetb Enrichment scorec q valued
Biological processes
 General processes
  GO:0006082 Organic acid metabolic process 298 64 2.686 0.0
  GO:0016053 Organic acid biosynthetic process 167 49 2.188 0.0
  GO:0044283 Small molecule biosynthetic process 226 56 1.965 0.0
  GO:1901362 Organic cyclic compound biosynthetic process 233 39 1.696 0.006043
  GO:0018130 Heterocycle biosynthetic process 223 37 1.7 0.008476
  GO:0019438 Aromatic compound biosynthetic process 199 38 1.984 0.000196
  GO:0046176 Aldonic acid catabolic process 4 3 5.8 0.033252
  GO:0040007 Growth 90 14 2.543 0.035375
 
 Nucleotide metabolism
  GO:0052803 Imidazole-containing compound metabolic process 12 6 5.887 0.011874
  GO:0034654 Nucleobase-containing compound biosynthetic process 138 22 2.025 0.013182
  GO:0055086 Nucleobase-containing small molecule metabolic process 124 26 1.901 0.015897
  GO:0042435 Indole-containing compound biosynthetic process 6 5 5.292 0.017839
  GO:0046112 Nucleobase biosynthetic process 9 6 4.451 0.022403
  GO:1901293 Nucleoside phosphate biosynthetic process 73 20 2.205 0.000229
  GO:0042430 Indole-containing compound metabolic process 11 7 7.289 0.000771
  GO:0009112 Nucleobase metabolic process 11 6 4.42 0.03223
 
 Amino acid metabolism
  GO:0006520 Cellular amino acid metabolic process 166 53 3.702 0.0
  GO:0008652 Cellular amino acid biosynthetic process 94 40 2.453 0.0
  GO:0009072 Aromatic amino acid family metabolic process 24 9 3.338 0.027736
  GO:0000105 Histidine biosynthetic process 8 6 3.642 0.035375
 
 Polysaccharide metabolism
  GO:0000271 Polysaccharide biosynthetic process 23 8 7.75 3.8e−05
  GO:0033692 Cellular polysaccharide biosynthetic process 19 7 8.4 7.7e−05
  GO:0044264 Cellular polysaccharide metabolic process 26 8 7.754 0.000214
  GO:0005976 Polysaccharide metabolic process 35 9 6.524 0.00034
  GO:0008653 Lipopolysaccharide metabolic process 12 6 5.546 0.003351
 
 Carbohydrate metabolism
  GO:1901135 Carbohydrate derivative metabolic process 178 29 1.95 0.008547
  GO:0046394 Carboxylic acid biosynthetic process 167 49 1.346 0.009947
  GO:0006757 ATP generation from ADP 15 4 4.938 0.028161
 
 Nitrogen and phosphate metabolism
  GO:0019637 Organophosphate metabolic process 147 25 2.12 0.008476
  GO:0044106 Cellular amine metabolic process 17 7 5.333 0.008547
  GO:0019627 Urea metabolic process 4 4 8.25 0.009169
  GO:0071941 Nitrogen cycle metabolic process 6 4 7.754 0.027141
  GO:0000050 Urea cycle 4 4 5.515 0.028161
  GO:0006793 Phosphorus metabolic process 244 34 1.602 0.042509
  GO:0006817 Phosphate ion transport 7 5 2.5 0.04326
 
 
Molecular functions
 GO:0016829 Lyase activity 93 21 3.246 0.000101
 GO:0016614 Oxidoreductase activity, acting on CH-OH group of donors 49 11 3.6 0.002604
 GO:0016879 Ligase activity, forming carbon-nitrogen bonds 42 12 1.907 0.008476
 GO:0048037 Cofactor binding 251 28 1.86 0.015897
 GO:0005315 Inorganic phosphate transmembrane transporter activity 4 3 10.533 0.018301
 GO:0016638 Oxidoreductase activity, acting on the CH-NH2 group of donors 8 4 8.333 0.024953
 GO:0042802 Identical protein binding 144 19 1.661 0.033252
 GO:0070279 Vitamin B6 binding 32 7 4.238 0.034385
a

Total number of genes associated with the GO term in the X. hortorum pv. vitians LM16734 genome.

b

Number of genes associated with the GO term in the subset of genes conditionally essential in planta.

c

The simplified formula for the enrichment score (without pseudocounts) is log[(b/q)/(m/p)], where b is the number of genes with the GO term in the subset, q is the number of genes in the subset with a parent of the GO term, m is the total number of genes with the GO term in the genome, and p is the number of genes in the genome with a parent of the GO term. Thus, the enrichment score is the log-transformed ratio of the two relative abundances of genes with the GO term compared to those with a parent GO term (i) in the subset and (ii) in the complete genome. The calculation was derived from the Ontologizer method (114).

d

Adjusted P value using the Benjamini-Hochberg false-discovery rate (FDR) test. GO terms with a q value of <0.05 were considered significantly enriched.