TABLE 2.

List of genes in each iModulon and published regulon and their direct targets

Response regulator	iModulon genesa	Targets from RegulonDBa	Direct targets
BaeR	baeR, mdtA, spy	acrD, baeR, baeS, mdtD, mdtA, mdtB, mdtC, spy	baeR, baeS, mdtD, mdtA, mdtB, mdtC, spy, intF, tnaA
CpxR	alx, baeR, cpxP, cpxR, dgcZ, ftnB, ldtC, mdtJ, raiA, tomB, yagU, yccA, yebE, yjfN, yncJ, yobB	acrD, aroG, bacA, baeR, baeS, bamE, cheA, cheW, cpxA, cpxP, cpxR, csgA, csgB, csgC, csgD, csgE, csgF, csgG, degP, dgcZ, dsbA, dsbC, efeU_2, fabZ, ftnB, hha, iceT, ldtC, ldtD, lpxA, lpxD, marA, marB, marR, mdtA, mdtB, mdtC, motA, motB, mscM, mzrA, ompC, ompF, ppiA, ppiD, psd, rpoE, rpoH, rseA, rseB, rseC, sbmA, skp, slt, spy, srkA, tomB, tsr, ung, yaiW, yccA, yebE, ygaU, yidQ, yqaE, yqjA	cpxA, cpxP, cpxR, yagU, yccA, fimA, fimI, lldD, lldR, ppiA, raiA, yceI
KdpE	kdpA, kdpB, kdpC, kdpD, kdpE	kdpA, kdpB, kdpC, kdpF	kdpA, kdpB, kdpC, adeP, uxaA, uxaC
PhoB	phoB, phoR, pstA, pstB, pstC, pstS	adiC, amn, argP, asr, cra, cusA, cusB, cusC, cusF, cusR, cusS, eda, feaR, gadW, gadX, hiuH, mipA, ompF, phnC, phnD, phnE_1, phnE_2, phnF, phnG, phnH, phnI, phnJ, phnK, phnL, phnM, phnN, phnO, phnP, phoA, phoB, phoE, phoH, phoQ, phoR, phoU, pitB, prpR, psiE, psiF, pstA, pstB, pstC, pstS, rspR, sbcC, sbcD, tktB, ugpA, ugpB, ugpC, ugpE, ugpQ, waaH, yegH, yhjC	phoB, phoR, pstA, pstB, pstC, pstS, phoU
ZraR	zraP, zraR	zraP, zraR, zraS	zraP, zraR, zraS, mgtA

^aBoldface genes in the “iModulon genes” and “Targets from RegulonDB” columns are shared genes.