Table 1.

Biological processes over-represented among four NYS S. Typhimurium lineages.

Lineagea	GO IDb	GO name	BH-adjusted P-valuec
I	GO:0042710	Biofilm formation	5.2E−13
I	GO:0048870	Cell motility	1.1E−03
I	GO:0090101	Negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	9.6E−03
II	GO:0009753	Response to jasmonic acid	3.9E−02
II	GO:0000746	Conjugation	3.9E−02
III	GO:0043473	Pigmentation	3.4E−07
III	GO:0000746	Conjugation	3.7E−07
III	GO:0043150	DNA synthesis involved in double-strand break repair via homologous recombination	4.0E−05
IV	GO:0019069	Viral capsid assembly	1.2E−26
IV	GO:0015694	Mercury ion transport	2.5E−10
IV	GO:0080167	Response to karrikin	6.5E−10
IV	GO:0044660	Cytolysis by virus via pore formation in host cell membrane	6.6E−10
IV	GO:0015074	DNA integration	4.1E−09
IV	GO:0019271	Aerobactin transport	1.3E−08
IV	GO:0044406	Adhesion of symbiont to host	4.7E−06
IV	GO:0009214	Cyclic nucleotide catabolic process	1.6E−04
IV	GO:0016998	Cell wall macromolecule catabolic process	2.5E−02
IV	GO:0006313	Transposition, DNA-mediated	2.6E−02

For a complete list of significant gene ontology (GO) terms in each lineage, including those referring to cellular components and molecular functions, as well as significant parent terms, see Supplementary Table S2.

^aLineages I (n = 37), II (n = 13), III (n = 14), and IV (n = 16).

^bGene Ontology (GO) identifier (ID).

^cP-values obtained using Ontologizer version 2.1 and adjusted to control for the false discovery rate (FDR) at the 0.05 level using the Benjamini–Hochberg procedure.