Predicted E. coli regulons

Regulons were predicted by clustering regulatory motifs that were detected by phylogenetic footprinting. The motifs used for clustering are those with statistical significance at p <= 0.2 as described in Genome Research, 12:1523-1532 and available at http://bayesweb.wadsworth.org/binding_sites. The clustering algorithm we used is BMC, described in Nature Biotech 21:435-443, but with the new feature of a sampling (or 50%) solution. Basically, the original algorithm found the clustering solution with the best (from among many seeds) log likelihood score. We have extended the algorithm to then take that "near optimal" clustering solution and iterate through the data, sampling motifs to determine if motifs are moving between clusters or sample into the same cluster repeatedly. The sampling solution of predicted regulons was used as data for the study described in Genome Research, 15:312-320 The even cluster models are here and the odd cluster models are here.

E582 19.369 | model | logo

```
purM-1 (upp) 	 500/500
```
```
yicE-1  	 500/500
```
```
purE-1  	 500/500
```
```
purR-1  	 500/500
```
```
yjcD-1  	 500/500
```
```
purH-3  	 500/500
```
```
cvpA-1  	 500/500
```
```
glyA-4  	 500/500
```
```
purL-2 (yfhD) 	 500/500
```

E583 18.918 | model | logo

```
lexA-1  	 500/500
```
```
dinI-1  	 500/500
```
```
b0959-2 (sulA) 	 500/500
```
```
uvrA-1  	 500/500
```
```
recA-1  	 500/500
```
```
uvrD-1  	 500/500
```
```
recN-2  	 500/500
```
```
yebG-2  	 500/500
```
```
dinP-1  	 500/500
```
```
ruvA-1  	 480/500
```

E594 15.682 | model | logo

```
nirB-3  	 500/500
```
```
yciD-3  	 500/500
```
```
focA-3  	 500/500
```
```
ung-2 (yfiD) 	 500/500
```
```
cydA-3  	 500/500
```
```
ndh-2  	 494/500
```
```
nrdD-1  	 470/500
```

E578 14.498 | model | logo

```
yaeD-1  	 500/500
```
```
metE-1  	 500/500
```
```
metF-1  	 500/500
```

E576 13.258 | model | logo

```
idnK-1  	 500/500
```
```
gntT-1  	 500/500
```
```
b2740-1  	 500/500
```

E592 13.228 | model | logo

```
udp-1 (ysgA) 	 500/500
```
```
ycdZ-1  	 500/500
```
```
mtlA-1  	 498/500
```
```
nagB-2 (nagE) 	 496/500
```
```
serA-1  	 453/500
```
```
fadD-1  	 200/500
```

E579 12.946 | model | logo

```
fabA-2  	 500/500
```
```
b2899-1  	 500/500
```

E595 12.545 | model | logo

```
trpR-1  	 500/500
```
```
mtr-1  	 500/500
```
```
trpE-1 (yciV) 	 500/500
```

E581 12.217 | model | logo

```
nrdD-2  	 500/500
```
```
nrdA-1  	 500/500
```

E587 11.923 | model | logo

```
tyrP-1  	 500/500
```
```
aroF-2  	 500/500
```
```
aroP-1  	 500/500
```

E591 11.283 | model | logo

```
malT-1  	 500/500
```
```
manX-1 (yoaE) 	 500/500
```
```
malX-1  	 500/500
```
```
ptsG-2  	 500/500
```
```
aqpZ-1  	 451/500
```
```
ptsH-1  	 326/500
```
```
gcl-1  	 237/500
```

E590 10.451 | model | logo

```
metB-3 (metJ) 	 437/437
```
```
metA-1  	 437/437
```
```
abc-1  	 379/437
```
```
metR-3  	 379/437
```

E1373 9.960 | model | logo

```
cdd-1  	 369/472
```
```
deoC-1  	 368/472
```
```
yjjN-1  	 339/472
```
```
mlc-1  	 321/472
```
```
glpA-1 (glpT) 	 318/472
```
```
cyaA-1 (hemC) 	 305/472
```
```
mglB-1  	 245/472
```

E577 9.450 | model | logo

```
fruB-1  	 500/500
```
```
epd-2  	 500/500
```
```
adhE-2  	 440/500
```

E589 9.014 | model | logo

```
thdF-1  	 500/500
```
```
fabF-3  	 500/500
```
```
lpdA-3  	 391/500
```

E567 8.724 | model | logo

```
ybeD-1  	 500/500
```
```
gcvA-5  	 500/500
```
```
pyrH-2  	 500/500
```
```
rnk-1  	 495/500
```

E586 8.541 | model | logo

```
nadB-1  	 500/500
```
```
uvrB-2  	 500/500
```
```
nuoA-2  	 500/500
```

E4565 8.452 | model | logo

```
yebK-1  	 364/364
```
```
yhdG-3  	 363/364
```
```
purR-3  	 361/364
```
```
hemC-1  	 349/364
```

E596 8.150 | model | logo

```
ilvB-2  	 500/500
```
```
mutM-2  	 500/500
```
```
secE-3  	 498/500
```
```
ychM-1  	 278/500
```
```
yjcX-1  	 252/500
```

E2984 7.723 | model | logo

```
b2531-1  	 417/418
```
```
mhpT-4  	 416/418
```
```
sucC-1  	 415/418
```
```
rpoD-3  	 121/418
```

E574 7.543 | model | logo

```
yigN-3  	 500/500
```
```
radC-1  	 500/500
```
```
fadD-1  	 235/500
```

E5010 7.530 | model | logo

```
ylcA-1 (ylcB) 	 348/349
```
```
lpdA-2  	 344/349
```
```
fur-2  	 334/349
```
```
dksA-1  	 321/349
```
```
cyoA-2  	 298/349
```
```
cydD-1  	 91/349
```

E726 7.313 | model | logo

```
edd-1  	 430/436
```
```
aroG-1 (b0753) 	 430/436
```
```
ybiF-1  	 430/436
```

E571 7.236 | model | logo

```
acrR-1  	 500/500
```
```
acrA-1  	 500/500
```

E580 7.199 | model | logo

```
b2595-2 (sfhB) 	 500/500
```
```
yihK-1  	 499/500
```

E570 7.119 | model | logo

```
acrA-2  	 500/500
```
```
envR-1  	 500/500
```

E4228 4.110 | model | logo

```
yjdF-1  	 194/333
```
```
yieP-1  	 193/333
```
```
infA-1  	 191/333
```
```
gltX-1  	 139/333
```

E3574 2.937 | model | logo

```
b1627-2  	 129/260
```
```
uraA-1  	 128/260
```

E2290 0.113 | model | logo

```
rpoC-1  	 245/253
```

E1022 0.075 | model | logo

```
rpsF-1  	 251/269
```

E421 0.010 | model | logo

```
rpoB-4  	 366/402
```

E6401 0.007 | model | logo

```
ftsZ-1  	 262/265
```

E5399 0.004 | model | logo

```
yccA-1  	 250/336
```
```
aspC-1  	 87/336
```

E6842 0.003 | model | logo

```
soxR-1 (soxS) 	 236/283
```

E350 0.001 | model | logo

```
rplM-2  	 151/281
```
```
dniR-2  	 130/281
```

E495 0.000 | model | logo

```
pheS-1  	 352/352
```

E5883 0.000 | model | logo

```
acnA-1  	 320/320
```

E3521 0.000 | model | logo

```
lepA-1  	 392/400
```

E417 0.000 | model | logo

```
rpsM-1  	 500/500
```

E414 0.000 | model | logo

```
rpsT-1  	 304/304
```

E453 0.000 | model | logo

```
ribB-1 (b3042) 	 500/500
```

E7108 0.000 | model | logo

```
dnaJ-2  	 279/279
```

E3150 0.000 | model | logo

```
rpmB-2  	 412/412
```

E2795 0.000 | model | logo

```
pssA-2  	 301/301
```

E372 0.000 | model | logo

```
nuoN-3  	 500/500
```

E440 0.000 | model | logo

```
yqaB-1  	 500/500
```

E404 0.000 | model | logo

```
yhgF-1  	 500/500
```

E330 0.000 | model | logo

```
atpF-1  	 500/500
```

E669 0.000 | model | logo

```
pheA-3  	 496/496
```

E452 0.000 | model | logo

```
rplJ-4  	 500/500
```

E370 0.000 | model | logo

```
hupB-1  	 500/500
```

E449 0.000 | model | logo

```
alaS-2  	 285/286
```

E389 0.000 | model | logo

```
folD-1  	 500/500
```

E6271 0.000 | model | logo

```
yhbY-3  	 307/307
```

E4911 0.000 | model | logo

```
yciL-1  	 296/296
```

E310 0.000 | model | logo

```
ybaU-1  	 404/405
```

E428 0.000 | model | logo

```
cdsA-1  	 500/500
```

E739 0.000 | model | logo

```
mhpT-1  	 273/494
```
```
lpxC-2  	 183/494
```

E307 0.000 | model | logo

```
coaA-1  	 500/500
```

E501 0.000 | model | logo

```
pheA-1  	 500/500
```

E650 0.000 | model | logo

```
rpsM-6  	 497/497
```

E4028 0.000 | model | logo

```
hflB-3  	 370/383
```

E376 0.000 | model | logo

```
pyrG-2  	 500/500
```

E318 0.000 | model | logo

```
thiC-3  	 500/500
```

E319 0.000 | model | logo

```
plsX-2  	 315/315
```

E5017 -0.002 | model | logo

```
atpG-1  	 349/349
```

E331 -0.002 | model | logo

```
cysW-2  	 294/294
```

E490 -0.002 | model | logo

```
trxB-1  	 350/350
```

O641 14.936 | model | logo

```
ygdP-1  	 500/500
```
```
uvrB-1  	 500/500
```
```
mutH-1  	 500/500
```

O649 14.443 | model | logo

```
fepB-1  	 500/500
```
```
cirA-1  	 499/500
```
```
b2392-1 (nupC) 	 498/500
```
```
ydiC-1  	 472/500
```
```
gpmA-1  	 449/500
```
```
yqjI-1  	 436/500
```
```
b1821-1  	 413/500
```
```
fecI-1  	 373/500
```
```
sodA-1  	 309/500
```

O648 12.693 | model | logo

```
lldP-1  	 500/500
```
```
pdhR-1  	 500/500
```
```
ung-1 (yfiD) 	 498/500
```

O646 10.928 | model | logo

```
glnL-2  	 500/500
```
```
yihK-4 (glnA) 	 500/500
```
```
ybhK-2  	 313/500
```

O647 10.579 | model | logo

```
xylF-2  	 500/500
```
```
xylA-1  	 500/500
```
```
ybiJ-2  	 498/500
```
```
oxyR-2  	 283/500
```

O636 10.200 | model | logo

```
ycbG-1  	 500/500
```
```
b0955-1  	 500/500
```
```
prsA-4  	 474/500
```

O640 9.454 | model | logo

```
glyA-2  	 500/500
```
```
ytfE-1  	 500/500
```
```
yciD-2  	 456/500
```

O638 9.382 | model | logo

```
pitB-1  	 500/500
```
```
pitA-1  	 500/500
```

O2225 9.291 | model | logo

```
fadB-1 (pepQ) 	 263/276
```
```
nhaB-1 (fadR) 	 260/276
```
```
ygjL-1  	 260/276
```
```
iclR-1 (metH) 	 251/276
```
```
glcD-1 (glcC) 	 217/276
```
```
b2342-1  	 209/276
```

O645 9.211 | model | logo

```
yhdG-2  	 318/319
```
```
purH-1  	 317/319
```
```
pykF-1  	 317/319
```
```
ycaD-1  	 135/319
```

O7434 7.595 | model | logo

```
ssb-1 (uvrA) 	 314/316
```
```
pldB-1 (yigK) 	 309/316
```
```
dnaQ-2 (rnhA) 	 264/316
```
```
ygdP-2  	 192/316
```
```
artP-1  	 136/316
```

O631 7.379 | model | logo

```
udhA-1 (yijC) 	 268/269
```
```
yhhZ-1  	 267/269
```
```
nadA-2  	 253/269
```
```
slyX-1 (fkpA) 	 183/269
```
```
yiaU-1  	 99/269
```

O642 6.713 | model | logo

```
pepA-1 (yjgP) 	 500/500
```
```
pssR-3 (yifE) 	 500/500
```

O6105 6.618 | model | logo

```
ygjV-1  	 352/352
```
```
kduI-1  	 352/352
```

O467 0.305 | model | logo

```
yhbL-1  	 229/251
```

O4281 0.219 | model | logo

```
accB-1  	 246/265
```

O4770 0.102 | model | logo

```
moaA-1  	 257/283
```

O3885 0.036 | model | logo

```
rne-1  	 291/301
```

O7163 0.034 | model | logo

```
corA-1  	 320/323
```

O8244 0.024 | model | logo

```
yfjB-1  	 203/294
```
```
yihK-2  	 85/294
```

O419 0.005 | model | logo

```
yjjV-1  	 412/419
```

O1510 0.000 | model | logo

```
prsA-3  	 316/318
```

O8011 0.000 | model | logo

```
mopB-1 (yjeH) 	 300/300
```

O454 0.000 | model | logo

```
yfjB-1  	 297/297
```

O360 0.000 | model | logo

```
yidC-1  	 500/500
```

O1500 0.000 | model | logo

```
tufA-2  	 254/254
```

O413 0.000 | model | logo

```
nuoN-1  	 500/500
```

O391 0.000 | model | logo

```
ygaG-1  	 500/500
```

O470 0.000 | model | logo

```
slyD-1  	 500/500
```

O5771 0.000 | model | logo

```
map-3  	 361/361
```

O392 0.000 | model | logo

```
leuS-2  	 500/500
```

O498 0.000 | model | logo

```
rpmB-1  	 300/300
```

O474 0.000 | model | logo

```
rpsF-3  	 428/428
```

O5333 0.000 | model | logo

```
yggH-1  	 370/373
```

O396 0.000 | model | logo

```
aroH-2  	 326/326
```

O352 0.000 | model | logo

```
surA-1  	 500/500
```

O6981 0.000 | model | logo

```
rpsB-2 (map) 	 308/308
```

O477 0.000 | model | logo

```
corA-2  	 500/500
```

O489 0.000 | model | logo

```
rpoB-2  	 500/500
```

O8205 0.000 | model | logo

```
rpsT-2  	 295/295
```

O2770 0.000 | model | logo

```
ribB-3  	 251/251
```

O428 0.000 | model | logo

```
arcA-1  	 255/255
```

O3037 -0.001 | model | logo

```
rplN-1  	 290/428
```
```
yigL-2  	 139/428
```

O4574 -0.001 | model | logo

```
rplK-1  	 371/393
```

O9080 -0.002 | model | logo

```
cpxR-1  	 271/271
```