Table 2. Characteristics of proteins missing in expanded operon lists.

Profile element	Expanded short list	Expanded total list
Proteins not detected*	277	471
Corresponding mRNA detected	263†	383‡
Mean mRNA signal (arithmetic)§	5,560	1,840
Mean mRNA signal (geometric)	2,240	740
Mean number of tryptic peptides predicted	11.2	11.5
Membrane proteins (low estimate to high estimate)	64-82	92-143
Proteins of unknown function¶	30	134

The genes coding for proteins in the short list, total list, and list of all E. coli proteins were contained in 335, 868, and 2,583 operons composed of 681, 1,618, and 4,286 protein-coding genes, respectively. (Five protein-coding genes had no operon assignment.) The mean numbers of genes in the operons were 2.03, 1.86, and 1.66, respectively, and the numbers of these operons composed of a single gene were 188, 520, and 1,748, respectively.

^*For data on the 404 and 1,147 proteins detected in the short and total lists, see Table 1, columns 1 and 4, respectively.

^†One gene was not represented on Affymetrix GeneChips.

^‡Four genes were not represented on Affymetrix GeneChips.

^§When membrane proteins and proteins of unknown function were not considered, the corresponding values for arithmetic and geometric mean mRNA signal intensities for the remaining missing proteins were as follows: short list, 6,390 and 2,620, respectively; total list, 2,110 and 870, respectively.

^¶This is the same as open reading frames (19). The overlap between these and membrane proteins is as follows: expanded short list, 0-2; expanded total list, 1-19.