Gene expression analysis indicates extensive genotype-specific crosstalk between the conjugative F-plasmid and the E. coli chromosome

Table 2 "F-plasmid effect only" genes: similar effects of F-plasmid in both bacterial backgrounds

	Fold-change
gene	F/nonF (MG1655)	F/nonF (DH5α)	P (F-effect)	function
b0373	2.72	3.49	0.00048	IS3 element
b1171	4.01	4.03	0.00543	ORF
b2254*	5.20	2.12	0.00323	putative sugar transferase
b2255*	4.56	2.53	0.0068	putative transformylase
osmB	2.06	3.92	0.0041	osmotically inducible lipoprotein
*Protein-A*	77.75	80.04	0.00001	sopA
*Protein-B*	16.18	12.71	0.00405	sopB
*Protein-C*	6.76	9.96	0.00004	repC (replication protein)
*Protein-E*	11.49	19.49	0.00553	repE (replication initiation protein)
*Protein-G*	36.00	15.14	0.00005	ccdB (letD) post-segregational killing
*Protein-H*	26.80	26.87	0.00001	ccdA (letA) suppression of ccdB
*traD*	168.46	127.67	0.00008	DNA transport
*traI*	11.57	15.46	0.00003	oriT nicking and unwinding
*trbH*	24.69	24.78	0.00015	unknown
metU	-4.09	-2.56	0.02676	Methionine tRNA; duplicate gene
yqgB	-2.60	-2.49	0.02466	ORF

* genes are members of the same operon.
Negative fold-change values indicate down-regulation in F-plasmid free cells.
Genes given in bold are coded on the F-plasmid. Note that the genes were called absent, but rather than setting the expression to zero, we used the hybridization signal detected to calculate the ratio between cells with and without F-plasmid.