Table 2.

Genes That Are Most Correlated With yjaX's Expression Pattern Across All 116 Experiments

Genea
Gene descriptionb
Pathwayc
RyjaXd
Se
Locationf
Operong
yjaX fabHA: 3-oxoacyl-acyl-carrier protein synthase III A FAS 1 21.2 — 70 1
yjaY fabF: 3-oxoacyl-acyl-carrier protein synthase II FAS 0.8481 21.2 1
yhfB fabHB: 3-oxoacyl-acyl-carrier protein synthase III B FAS 0.7798 17.2 — 51 2*
gltT H+/Na+-glutamate symport protein 0.7405 3
fabD Malonyl CoA-acyl carrier protein transacylase FAS 0.7253 16.7 4
accB Acetyl-CoA carboxylase (biotin carboxyl carrier subunit) FAS 0.7147 5
yhdO plsC: 1-acylglycerol-3-phosphate O-acyltransferase PLS 0.7007 15.5 — 72 6*
ylpC Unknown; similar to unknown proteins 0.6731 16.7 — 34 4
fabG β-ketoacyl-acyl carrier protein reductase FAS 0.6624 16.7 4
yxlF Similar to ABC transporter (ATP-binding protein) 0.6601 7*
panD Aspartate 1-decarboxylase PAN 0.6412 8
yjbW fabl: enoyl-acyl-carrier protein reductase FAS 0.6360 17.9 — 17 9*
panB Ketopantoate hydroxymethyltransferase PAN 0.6356 8
ylmB Similar to acetylornithine deacetylase 0.6318 10
plsX Involved in fatty acid/phospholipid synthesis PLS 0.6279 16.7 4
yraK Predicted hydrolase/acyl-transferase 0.6277
azlD Branched-chain amino acid transport 0.6271
ykoK Similar to Mg2+ transporter 0.6224
yobL Unknown; similar to unknown proteins from B. subtilis 0.6214
yrhI
Unknown; similar to transcriptional regulator (TetR/AcrR family)
0.6188

a The commonly used gene name

b A description of the gene product's function

c The genes already known to be involved in type II FAS and connected pathways (PAN, pantothenate biosynthesis; PLS, phospholipid biosynthesis)

d The correlation coefficient RyjaX

e The similarity score S for possible transcription-factor-binding sites in upstream sequences of the coregulated transcriptional units (averages of the scores S arising from matches with the palindromic motif on both DNA strands, see Methods), bold numbers indicating the operon head genes

f The genomic location of the those motifs, counted in base pairs upstream from the translation-start codon of the operon head gene

g The references to corresponding transcription units, with same numbers indicating the same operons (see text). A superscript star indicates isolated genes, without neighboring genes being coexpressed