Toxicogenomic analysis incorporating operon-transcriptional coupling and toxicant concentration-expression response: analysis of MX-treated Salmonella

Ward, William O; Swartz, Carol D; Porwollik, Steffen; Warren, Sarah H; Hanley, Nancy M; Knapp, Geremy W; McClelland, Michael; DeMarini, David M

doi:10.1186/1471-2105-8-378

Table 2 Analysis of genes considered differentially expressed on the 54 operons identified by the operon analysis

From: Toxicogenomic analysis incorporating operon-transcriptional coupling and toxicant concentration-expression response: analysis of MX-treated Salmonella

Operon number*	Number of genes in operon	Smallest p-value^†	FC^‡	Largest p-value^§	FC^¶	% In same direction^¥	% with p < 0.05	% Missing genes^#
1123^π	6	4.94E-02	-1.9	0.21	1.5	17	17	17
865	4	2.83E-02	-1.9	0.73	1.1	25	25	25
369	3	4.65E-02	-1.6			33	33	67
1604	4	2.57E-02	2.0	0.18	1.7	50	25	50
617	2	3.59E-02	2.2	0.85	-1.1	50	50	0
638	2	1.19E-02	2.4			50	50	50
747	2	4.13E-02	1.7	0.65	-1.1	50	50	0
1603	4	1.83E-02	3.2	0.02	3.2	50	50	50
2136	2	4.94E-02	-1.6	0.41	1.2	50	50	0
435	6	9.90E-03	-2.1	0.80	1.1	67	17	17
562	3	2.20E-03	7.5	0.97	1.0	67	33	33
1586	3	5.47E-03	3.1	0.39	-1.3	67	33	0
2535	3	2.38E-03	2.4	0.13	1.5	67	33	33
2213^π	7	1.65E-02	-3.7	0.02	-3.7	71	29	0
1301	11	4.01E-02	2.7	0.86	-1.1	73	9	18
35	4	4.92E-02	1.9	0.80	-1.1	75	25	0
1014	4	3.48E-02	-1.7	0.48	1.3	75	25	0
619	4	2.28E-02	2.3	0.57	-1.1	75	75	0
867	13	1.05E-02	-2.2	0.20	1.4	77	15	8
1279	20	4.36E-02	1.6	0.59	-1.2	80	5	5
374	5	4.26E-02	2.3	0.64	-1.1	80	20	0
615	5	3.13E-03	5.1	0.68	1.1	80	60	20
119	6	1.77E-02	3.0	0.81	-1.1	83	17	0
1754	6	4.62E-02	1.7	0.88	1.1	83	17	17
866	9	1.45E-02	-1.9	0.84	1.1	89	22	0
1275	20	3.33E-02	-1.6	0.54	-1.1	100	10	0
2495	6	4.39E-02	2.9	1.00	1.0	100	17	0
858	4	3.87E-02	-1.8	0.18	-1.4	100	25	0
868	4	4.73E-02	-1.7	0.65	-1.2	100	25	0
336	3	2.46E-02	-1.8	0.52	-1.1	100	33	0
1090	3	4.84E-02	-1.6	0.11	-1.5	100	33	0
1508	6	7.64E-03	-2.0	0.50	-1.2	100	33	0
2178	3	3.87E-02	-1.8	0.72	-1.1	100	33	0
2384	3	3.69E-02	1.7	0.08	1.5	100	33	0
62	2	1.03E-03	2.8	0.31	1.3	100	50	0
441	2	6.63E-04	4.8	0.53	1.2	100	50	0
543	2	5.49E-03	3.5	0.50	1.2	100	50	0
1201	2	3.66E-03	2.2	0.11	1.4	100	50	0
1376	2	4.88E-02	46.2	0.24	1.6	100	50	0
2181	4	2.91E-02	-1.7	0.08	-1.5	100	50	0
2389	2	5.75E-03	2.	0.35	1.4	100	50	0
722	9	1.65E-02	-2.0	0.12	-1.5	100	67	0
1284	3	3.83E-02	-2.7	0.05	-2.8	100	67	0
1499	4	2.70E-02	2.4	0.07	1.8	100	75	0
1761	4	1.33E-03	4.2	0.63	1.1	100	75	0
550	4	7.51E-04	4.1	0.05	2.1	100	100	0
789	2	4.21E-02	-1.6	0.45	-1.5	100	100	0
881	2	2.67E-04	3.1	0.01	2.0	100	100	0
911	2	4.46E-02	-2.3	0.05	-1.9	100	100	0
1260	2	8.08E-06	8.6	0.00	14.3	100	100	0
1652	3	2.79E-05	14.8	0.01	2.6	100	100	0
1705	2	3.15E-02	-1.7	0.04	-1.6	100	100	0
1766	2	2.73E-03	2.7	0.01	2.6	100	100	0
2411	2	4.47E-03	2.4	0.01	1.8	100	100	0

*Table 3 contains a list of the genes in each of these operons.
^†The lowest p-value from the CyberT analysis in each operon comparing the high concentration of MX (4.6 μM) to the control.
^‡The fold change for the transcript with the lowest p-value in the operon.
^§ The p-value for the transcript with the highest p-value in the operon.
^¶ The fold change for the transcript with the highest p-value in the operon.
^¥The percent of transcripts in the operon with the same direction of change as the transcript with the lowest p-value in the operon.
^#The percent of genes where the intensity measurements were equal to or less than background.
^πThese operons had the majority of their genes expressing in the direction opposite that of a gene with a p-value < 0.05. Operon #2213 had two genes with p-values < 0.05 that changed in opposite directions.

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ISSN: 1471-2105

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