GenExpdb_OKID	Similarity2HmfAvsHmfAnb_upregulated_pgenes	Similarity2HmfAvsHmfAnb_downregulated_pgenes	GenExpdb_description_condition
28	-231.016222	-261.9114641	WT 5 min after 1 min UV treatment / WT 0 min before UV treatment
29	-61.54978086	-113.5562725	lexA 5 min after 1 min UV treatment / WT 0 min before UV treatment
30	-332.0968543	-294.0590009	WT 10 min after 1 min UV treatment / WT 0 min before UV treatment
31	-43.59688934	-96.75774208	lexA 10 min after 1 min UV treatment / WT 0 min before UV treatment
32	-308.8566256	-402.0123918	WT 20 min untreated cells / WT 0 min before UV treatment
33	-422.158033	-333.2544362	WT 20 min after 1 min UV treatment / WT 0 min before UV treatment
34	10.92887545	2.102471453	lexA 20 min untreated cells / WT 0 min before UV treatment
35	-61.78475508	-99.15153369	lexA 20 min after 1 min UV treatment / WT 0 min before UV treatment
36	-291.4904122	-187.9716209	WT 40 min after 1 min UV treatment / WT 0 min before UV treatment
37	-85.99386049	-123.0515116	lexA 40 min after 1 min UV treatment / WT 0 min before UV treatment
38	-314.1943734	-375.3782353	WT 60 min untreated cells / WT 0 min before UV treatment
39	-197.9534201	-162.6860039	WT 60 min after 1 min UV treatment / WT 0 min before UV treatment
40	-10.97572627	-3.050289028	lexA 60 min untreated cells / WT 0 min before UV treatment
41	-103.3279414	-119.8082761	lexA 60 min after 1 min UV treatment / WT 0 min before UV treatment
42	-1.563788471	-17.25317215	lexA 0 min before UV treatment / WT 0 min before UV treatment 
43	3.987821106	159.0406828	10 min with 0.3 ug/ml mitomycin C / 0 min no MMC
44	93.77127445	108.1269203	25 min with 0.3 ug/ml mitomycin C / 0 min no MMC
45	85.94378284	107.4352353	40 min normal growth / 0 min normal growth
46	199.0473263	396.8752574	40 min with 0.3 ug/ml mitomycin C / 0 min no MMC
47	132.5602779	458.2136893	10 min exposure to 3.0 ug/ml mitomycin C followed by 50 min growth / 0 min no MMC
48	117.1624964	502.2647361	10 min exposure to 3.0 ug/ml mitomycin C followed by 70 min growth / 0 min no MMC
49	110.8876037	172.9739731	80 min normal growth / 0 min normal growth
50	125.1606195	175.9188975	80 min with 0.3 ug/ml mitomycin C / 0 min no MMC
54	-63.56689628	-23.48863444	appY Aerobic / WT Aerobic
55	-22.0512357	-17.13163022	arcA Aerobic / WT Aerobic
56	-19.03316566	10.18883826	arcA fnr Aerobic / WT Aerobic
57	63.0556273	37.19707858	fnr Aerobic / WT Aerobic
58	-20.21135794	48.89456506	oxyR Aerobic / WT Aerobic
59	-38.49574016	-22.43630279	soxS Aerobic / WT Aerobic
60	-163.6175675	-60.16100397	appY Anaerobic / WT Anaerobic
61	259.1262982	15.77825052	arcA Anaerobic / WT Anaerobic
62	435.0018345	133.9816036	arcA fnr Anaerobic / WT Anaerobic
63	157.3866026	58.67837307	fnr Anaerobic / WT Anaerobic
64	-15.93653228	-25.57805299	oxyR Anaerobic / WT Anaerobic
65	-159.421708	-87.55800004	soxS Anaerobic / WT Anaerobic
66	-89.03071023	9.160206469	Anaerobic WT / Aerobic WT
67	-97.05611726	39.57531988	MG1655 + F-plasmid / MG1655
68	123.2046553	353.1314509	DH5-alpha + F-plasmid / DH5-alpha
69	-49.0108071	-78.77108107	melR* / melR mutant
70	-165.1245207	469.3940288	mRNA abundance WT on LB / Genomic DNA from dnaC(ts) mutant
71	119.5180259	-516.1515795	mRNA abundance WT on LB / Genomic DNA from dnaC(ts) mutant (dye swap)
72	298.5715901	-342.4726148	mRNA abundance gyrA D82G mutant on LB / Genomic DNA from dnaC(ts) mutant
73	171.1605523	-378.6714651	mRNA abundance gyrA D82G mutant on LB / Genomic DNA from dnaC(ts) mutant (dye swap)
74	43.94648486	-307.8940767	"mRNA abundance (wt in LB, norfloxacin for 10 min)  / Genomic DNA from dnaC(ts) mutant"
75	103.60478	-312.2401979	"mRNA abundance (wt in LB, norfloxacin for 10 min) / Genomic DNA from dnaC(ts) mutant (dye swap)"
76	274.893841	-422.801576	"mRNA abundance (wt in LB, norfloxacin for 30 min) / Genomic DNA from dnaC(ts) mutant"
77	198.8948718	-335.9874745	"mRNA abundance (wt in LB, norfloxacin for 30 min) / Genomic DNA from dnaC(ts) mutant (dye swap)"
78	-20.05727273	61.27866599	"mRNA abundance (gyrA D82G, LB) / mRNA abundance (wt, LB)"
79	12.02529241	-57.44614189	"mRNA abundance (gyrA D82G, LB) / mRNA abundance (wt, LB) (dye swap)"
80	6.016508409	25.75029502	"mRNA abundance (wt, M9) / Genomic DNA from dnaC(ts) mutant"
81	-25.8135495	190.7739296	2mM copper / no added copper
82	-108.9516807	-348.3116742	0.75mM added copper / no added copper
83	10.98550606	-31.56753923	no added copper / no added copper
84	24.77489386	51.19507314	DM medium / LB medium
85	160.6782473	33.50509465	glycerol / glucose
86	30.60065397	-41.53633629	succinate / glucose
87	404.4946558	114.9011214	alanine / glucose
88	581.1092055	136.8960423	acetate / glucose
89	641.0517571	174.947102	proline / glucose
90	19.95041841	82.28206512	Aerobic steady-state 200uM GSNO for 5 minutes / No GSNO (Chemostat 1)
91	62.84098243	1.794284064	Aerobic steady-state 200uM GSNO for 5 minutes / No GSNO (Chemostat 1 dye swap)
92	156.9457221	112.0682707	Aerobic steady-state 200uM GSNO for 5 minutes / No GSNO (Chemostat 2)
93	63.17126298	75.61057217	Aerobic steady-state 200uM GSNO for 5 minutes / No GSNO (Chemostat 2 dye swap)
94	-33.75425459	27.06833168	SAnaerobic steady-state 200uM GSNO for 5 minutes / No GSNO (Run 1)
95	-89.80599914	164.1156358	Anaerobic steady-state 200uM GSNO for 5 minutes / No GSNO (Run 1 dye swap)
96	-30.23984698	76.32138711	Anaerobic steady-state 200uM GSNO for 5 minutes / No GSNO (Run 2)
97	-48.02718626	58.86799931	Anaerobic steady-state 200uM GSNO for 5 minutes / No GSNO (Run 2 dye swap)
98	10.47710874	157.4408783	5 min sigma32 induction / Control
99	-112.4465069	239.5565413	10 min sigma32 induction / Control
100	-148.4348754	248.3380246	15 min sigma32 induction / Control
101	21.28586026	142.3819603	IS5 deletion / WT Motile strain
102	-16.48618222	-152.8865314	IS5 deletion / WT Non-motile strain
103	-88.72907505	-403.1590493	WT Non-motile strain / WT Motile strain
104	-86.76352255	439.2053889	PHMB exposed  / unexposed
105	7.713753675	-207.6437675	dam / WT
106	40.68404759	-86.03894255	dam mutS / WT
107	52.17702712	-65.73627554	mutS / WT
108	-97.53333022	-401.8046475	dam  / WT
109	-88.02164469	-271.5775817	dam mutS  / WT
110	14.35461844	-263.2124989	mutS  / WT
111	-178.856942	-254.1885492	"dam mutS, cisplatin treated / WT cisplatin treated"
112	-289.5935939	-361.3411945	"dam, cisplatin treated / WT cisplatin treated"
113	160.9104588	-46.12449062	"mutS, cisplatin treated / WT cisplatin treated"
114	-63.27076651	14.99451475	WT pBAD-ryhB / WT pNM12 control
115	-10.11515979	-10.34526397	fur pBAD-ryhB  / fur pNM12 control
116	-48.09689598	76.6342027	WT pBAD-ryhB +FeSO4 + / WT pNM12 control +FeSO4
117	-262.3066353	-77.83645606	rne pRNG3 / WT pPM30
118	-226.6823687	182.3448042	rne pNRNE5 / WT pPM30
119	-5.816455174	-64.12857581	rng / WT pPM30 Trial A
120	-137.4736425	-114.6460995	rne pBADRNE / WT pPM30
121	-9.547238464	-67.88684729	WT pRNG3 / WT pPM30
122	39.38870853	8.711886802	rng / WT pPM30 Trial B
123	-196.5711717	-203.9623817	rne pBAD-RNE without Arabinose / WT
159	25.78182893	-3.136671756	WT + Leu / WT - Leu
160	203.2792791	162.6456198	lrp + Leu / WT - Leu
161	181.5498085	172.5443878	lrp - Leu / WT - Leu
162	68.83310407	43.23612081	lrp + Leu / lrp - Leu
163	-88.94162045	-9.96014936	RpoE induced (2.5 min) / Wild type control (2.5 min) Expt 3
164	-9.41211304	-234.1883038	RpoE induced (2.5 min) / Wild type control (2.5 min) Expt 4
165	-2.441914806	91.7598544	RpoE induced (5 min) / Wild type control (5 min) Expt 1
166	-12.14993675	-1.741526927	RpoE induced (5 min) / Wild type control (5 min) Expt 2
167	-13.57715118	-40.55861981	RpoE induced (5 min) / Wild type control (5 min) Expt 3
168	-70.062138	-244.6450034	RpoE induced (5 min) / Wild type control (5 min) Expt 4
169	-81.62734385	-137.0180459	RpoE induced (10 min) / Wild type control (10 min) Expt 3
170	-58.28220904	-228.6152923	RpoE induced (10 min) / Wild type control (10 min) Expt 4
171	12.29498813	-48.62001596	RpoE induced (15 min) / Wild type control (15 min) Expt 1
172	-51.48844244	-83.87707512	RpoE induced (15 min) / Wild type control (15 min) Expt 2
173	-65.89557204	-24.04116772	RpoE induced (20 min) / Wild type control (20 min) Expt 3
174	-42.68806551	127.3857963	RpoE induced (20 min) / Wild type control (20 min) Expt 4
175	-45.8694667	-46.16472142	RpoE induced (30 min) / Wild type control (30 min) Expt 2
176	-71.27260386	-111.806079	RpoE induced (30 min) / Wild type control (30 min) Expt 3
177	-92.54021536	-89.22484229	RpoE induced (60 min) / Wild type control (60 min) Expt 3
178	-10.79213826	-215.2868763	RpoE induced (30 min) / Wild type control (30 min) Expt 4
179	10.36972428	18.44452729	RpoE induced (60 min) / Wild type control (60 min) Expt 1
180	-63.40237427	-20.36301145	RpoE induced (60 min) / Wild type control (60 min) Expt 2
181	-156.4746547	-349.8379124	RpoE induced (60 min) / Wild type control (60 min) Expt 4
182	5.313019537	-59.0456072	RpoE induced (0 min) / Wild type control (0 min) Expt 3
183	-22.15506693	-85.15908341	RpoE induced (0 min) / Wild type control (0 min) Expt 4
184	-193.0341662	142.9116409	ydgG / WT
185	20.36194214	279.0722899	fnr- aerobic / aerobic reference
186	-22.81903159	-113.6463888	WT aerobic / aerobic reference
187	401.8316536	341.2291205	fnr- anaerobic / aerobic reference
188	88.18521901	-80.53361757	WT anaerobic / aerobic reference
189	552.4613287	566.5041055	fnr- anaerobic + NO2 / aerobic reference
190	88.89333419	-89.73060718	WT anaerobic + NO2 / aerobic reference
191	301.8094262	418.1621299	fnr- anaerobic + NO3 / aerobic reference
192	86.39070357	-91.45807556	WT anaerobic + NO3 / aerobic reference
193	-122.4671696	97.79146326	fnr- aerobic / anaerobic reference
194	-257.9163154	-138.0624454	WT aerobic / anaerobic reference
195	125.963548	390.2517666	fnr- anaerobic / anaerobic reference
196	-97.61076834	-42.53275558	WT anaerobic / anaerobic reference
197	241.6650104	696.7395507	fnr- anaerobic + NO2 / anaerobic reference
198	-67.55198117	0.40854015	WT anaerobic + NO2 / anaerobic reference
199	136.0221202	382.7271745	fnr- anaerobic + NO3 / anaerobic reference
200	-115.7999064	-98.91162939	WT anaerobic + NO3 / anaerobic reference
201	44.85740681	-1.108166954	narXL anaerobic + NO2 / anaerobic reference
202	95.22513722	209.6831599	narXLP anaerobic + NO2 / anaerobic reference
203	31.02587186	162.8473196	WT 20 gL EtOH / WT 0 gL EtOH
204	85.79926832	291.5544635	WT 40 gL EtOH / WT 0 gL EtOH
205	-239.8176087	-114.8493523	WT biofilm after 7h of culturing / WT biofilm after 4h of culturing
206	-223.8603887	-84.60946683	WT after 7h of suspension culture  / WT after 4h of suspension culture
207	-1.46582541	116.4600413	WT biofilm after 15h of culturing / WT biofilm after 4h of culturing
208	-153.7135749	58.66509594	WT after 15h of suspension culture / WT after 4h of suspension culture
209	-75.4251164	251.6568685	WT biofilm after 24h of culturing / WT biofilm after 4h of culturing
210	-184.5917825	320.1464442	WT after 24h of suspension culture / WT after 4h of suspension culture
211	-91.87352196	-48.93901758	WT biofilm after 4h of culturing / WT after 4h of suspension culture
212	-134.1093801	-65.52612148	WT biofilm after 7h of culturing / WT after 7h of suspension culture
213	51.92766951	40.38810202	WT biofilm after 15h of culturing / WT after 15h of suspension culture
214	-2.969718255	0.9407708	WT biofilm after 24h of culturing / WT after 24h of suspension culture
215	87.45826563	191.6112645	yceP biofilm / WT biofilm
216	-95.43098882	114.2118752	yliH biofilm / WT biofilm
217	6.122866981	39.6884281	dpiA overexpressor/ wt
218	-18.91122838	135.3021358	dpiA 2-fold overexpressor/ wt
219	72.98243859	85.80304367	RpoH induced (2.5 min) / Wild type control (2.5 min)
220	52.68041084	32.84233418	RpoH induced (5 min) / Wild type control (5 min)
221	23.15584701	4.010107227	RpoH induced (10 min) / Wild type control (10 min)
222	-37.43812033	-28.75708152	RpoH induced (20 min) / Wild type control (20 min)
223	99.95687431	105.9451399	RpoH induced (0 min) / Wild type control (0 min)
224	-93.50042826	-83.05806542	WT M9 2 min post rif / WT M9
225	-57.90595171	119.1642018	WT LB 2 min post rif / WT LB
226	-85.54893717	-29.11817676	WT M9 4 min post rif / WT M9
227	-24.50487241	251.6801666	WT LB 4 min post rif / WT LB
228	12.61011617	409.3682541	WT LB 6 min post rif / WT LB
229	-65.71565038	76.49297622	WT M9 6 min post rif / WT M9
230	-21.10236988	89.56284326	WT M9 8 min post rif / WT M9
231	35.94277542	543.9780443	WT LB 8 min post rif / WT LB
232	383.3125871	-2.274176738	WT LB / Genomic DNA
233	578.9333156	-123.4977338	WT M9-glucose / Genomic DNA
234	-60.07545943	-76.74976282	15 min after Ampicillin (100 ug/ml) / 0 min before treatment
235	-37.23791757	-22.27785256	30 min after Ampicillin (100 ug/ml) / 0 min before treatment
236	-19.36568203	-24.49304756	45 min after Ampicillin (100 ug/ml) / 0 min before treatment
237	7.627811892	-5.373310089	60 min after Ampicillin (100 ug/ml) / 0 min before treatment
238	2.082093229	-17.41521717	75 min after Ampicillin (100 ug/ml) / 0 min before treatment
239	-148.9060306	-171.917307	0 min after Ampicillin (100 ug/ml) / 0 min before treatment
240	40.46011927	93.43007115	2 min timepoint washed in 0.1 M CaCl2 + 15 % glycerol / before washing in LB
241	62.74878335	58.21278966	5 min timepoint washed in 0.1 M CaCl2 + 15 % glycerol / before washing in LB
242	52.09251728	23.74744535	10 min timepoint washed in 0.1 M CaCl2 + 15 % glycerol / before washing in LB
243	45.19114116	35.043419	20 min timepoint washed in 0.1 M CaCl2 + 15 % glycerol / before washing in LB
244	39.22751737	73.51900479	40 min timepoint washed in 0.1 M CaCl2 + 15 % glycerol / before washing in LB
245	33.71464383	76.54467749	60 min timepoint washed in 0.1 M CaCl2 + 15 % glycerol / before washing in LB
246	-550.9956907	-487.1130723	15 min recovery from stationary phase LB + glucose / Bogel-Vonner OD 0.5
247	-540.7782249	-527.0713869	30 min recovery from stationary phase LB + glucose / Bogel-Vonner OD 0.5
248	-472.6563493	-440.1823685	45 min recovery from stationary phase LB + glucose / Bogel-Vonner OD 0.5
249	-461.5534538	-492.2437127	60 min recovery from stationary phase LB + glucose / Bogel-Vonner OD 0.5
250	-355.3764528	-479.2316525	75 min recovery from stationary phase LB + glucose / Bogel-Vonner OD 0.5
251	-235.0736279	-132.4762827	90 min recovery from stationary phase LB + glucose / Bogel-Vonner OD 0.5
252	-92.12956117	142.8387509	0 min recovery from stationary phase LB + glucose / Bogel-Vonner OD 0.5
253	-1.493178392	156.6396251	5 min after Indol-acrylate (10 ug/ml) / 0 min before treatment
254	-26.43476799	132.9648594	15 min after Indol-acrylate (10 ug/ml) / 0 min before treatment
255	-130.1983112	-79.5357463	30 min after Indol-acrylate (10 ug/ml) / 0 min before treatment
256	-110.8947473	-206.1016195	60 min after Indol-acrylate (10 ug/ml) / 0 min before treatment
295	101.1931487	237.9661535	2 min after Norfloxacin (50 ug/ml) / 0 min before treatment
296	61.27087968	183.8634914	5 min after Norfloxacin (50 ug/ml) / 0 min before treatment
297	103.2489029	322.9471115	10 min after Norfloxacin (50 ug/ml) / 0 min before treatment
298	122.8095574	473.0264714	20 min after Norfloxacin (50 ug/ml) / 0 min before treatment
299	75.19325266	410.3919005	30 min after Norfloxacin (50 ug/ml) / 0 min before treatment
300	50.74233884	-132.3466844	gyrA parC 2 min after Norfloxacin (15 ug/ml) / gyrA parC 0 min before treatment
301	-21.27665516	-268.382503	gyrA parC 5 min after Norfloxacin (15 ug/ml) / gyrA parC 0 min before treatment
302	-3.754690015	-199.9906532	gyrA parC 10 min after Norfloxacin (15 ug/ml) / gyrA parC 0 min before treatment
303	245.8098203	213.9117023	gyrA parC 20 min after Norfloxacin (15 ug/ml) / gyrA parC 0 min before treatment
304	219.17075	275.6780798	gyrA parC 30 min after Norfloxacin (15 ug/ml) / gyrA parC 0 min before treatment
305	9.150948489	-169.4476185	gyrA parC 2 min after Norfloxacin (50 ug/ml) / gyrA parC 0 min before treatment
306	73.35010841	-37.69225762	gyrA parC 5 min after Norfloxacin (50 ug/ml) / gyrA parC 0 min before treatment
307	43.01389415	-130.9046272	gyrA parC 10 min after Norfloxacin (50 ug/ml) / gyrA parC 0 min before treatment
308	288.2099113	159.4185478	gyrA parC 20min after Norfloxacin (50 ug/ml) / gyrA parC 0 min before treatment
309	240.4244577	209.7780885	gyrA parC 30 min after Norfloxacin (50 ug/ml) / gyrA parC 0 min before treatment
310	385.5939159	737.5298229	15 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5
311	446.0029938	821.597757	30 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5
312	358.5733734	760.0874794	45min recovery in 10mM Na-P / Bonner-Vogel OD~0.5
313	404.1018459	806.0105237	60 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5
314	364.6311875	779.4706416	75 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5
315	435.3035299	909.5272248	90 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5
316	342.4238449	654.4573367	0 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5
317	130.2435067	522.4282423	15 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5
318	93.23727382	558.8372811	30 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5
319	-5.922229074	490.1787394	45min recovery in 10mM Na-P / Bonner-Vogel OD~0.5
320	0.481607497	548.5219898	60 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5
321	-16.9818844	539.7507746	75 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5
322	35.48345887	533.9284745	90 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5
323	288.2738291	642.4741193	0 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5
324	-47.21663683	-428.4955854	5 min 0.01 M Sodium Azide treatment / 0 min before treatment in Bonner-Vogel
325	-38.36305546	-343.368721	15 min 0.01 M Sodium Azide treatment / 0 min before treatment in Bonner-Vogel
326	-36.80295674	-438.3699331	30 min 0.01 M Sodium Azide treatment / 0 min before treatment in Bonner-Vogel
327	-43.96399129	-375.9549935	60 min 0.01 M Sodium Azide treatment / 0 min before treatment in Bonner-Vogel
328	44.84464532	-360.8317391	OD 0.03 anaerobic growth in M9 + glucose / genomic DNA reference
329	192.0625823	10.36340258	OD 0.2 anaerobic growth in M9 + glucose / genomic DNA reference
330	229.5182415	41.51216813	OD 0.35 anaerobic growth in M9 + glucose / genomic DNA reference
331	309.2268915	37.6109434	OD 0.6 anaerobic growth in M9 + glucose / genomic DNA reference
332	290.3261786	29.75175909	OD 0.9 anaerobic growth in M9 + glucose / genomic DNA reference
333	185.8988169	59.68079301	stationary phase anaerobic growth in M9 + glucose / genomic DNA reference
334	48.27478496	-213.2608467	OD 0.05 anaerobic growth in M9 + glucose + fumarate / genomic DNA reference
335	97.1191619	-280.2878095	OD 0.21 anaerobic growth in M9 + glucose + fumarate / genomic DNA reference
336	169.7721223	-152.8657074	OD 0.43 anaerobic growth in M9 + glucose + fumarate / genomic DNA reference
337	132.5669556	-143.2661516	OD 0.7 anaerobic growth in M9 + glucose + fumarate / genomic DNA reference
338	21.78185608	-42.32351512	OD 1.2 anaerobic growth in M9 + glucose + fumarate / genomic DNA reference
339	73.47097956	-68.35656514	stationary phase anaerobic growth in M9 + glucose + fumarate / genomic DNA reference
340	-167.223969	-343.6869672	Anaerobic growth in M9 + glucose OD 0.08 / Aerobic OD 0.4
341	-142.7219141	-360.2432403	Anaerobic growth in M9 + glucose OD 0.15 / Aerobic OD 0.4
342	-59.15931849	-199.6535566	Anaerobic growth in M9 + glucose OD 0.34 / Aerobic OD 0.4
343	11.17707971	-126.4147573	Anaerobic growth in M9 + glucose OD 0.73 / Aerobic OD 0.4
344	-5.992829641	-106.742909	Anaerobic growth in M9 + glucose OD 1.02 / Aerobic OD 0.4
345	-117.4630183	161.3218988	Anaerobic growth in M9 + glucose OD 1.27 / Aerobic OD 0.4
346	32.52326289	-160.8219439	Anaerobic growth in M9 + glucose + fumarate OD 0.15 / Aerobic OD 0.4
347	50.01244079	-208.5261399	Anaerobic growth in M9 + glucose + fumarate OD 0.30 / Aerobic OD 0.4
348	134.3160967	-65.94682647	Anaerobic growth in M9 + glucose + fumarate OD 0.63 / Aerobic OD 0.4
349	135.3471677	-61.3549538	Anaerobic growth in M9 + glucose + fumarate OD 0.85 / Aerobic OD 0.4
350	121.1251925	-52.78935973	Anaerobic growth in M9 + glucose + fumarate OD 1.07 / Aerobic OD 0.4
351	-135.2201942	219.196651	Anaerobic growth in M9 + glucose + fumarate OD 1.29 / Aerobic OD 0.4
352	100.8812529	130.5767712	5 min after Gamma treatment / 0 min before treatment
353	161.4976463	173.8693216	10 min after Gamma treatment / 0 min before treatment
354	131.2409383	96.07401481	20 min after Gamma treatment / 0 min before treatment
355	92.38955182	95.56175837	40 min after Gamma treatment / 0 min before treatment
356	84.29171279	37.66062022	60 min after Gamma treatment / 0 min before treatment
357	47.45429036	-89.17175316	acrD- 5 min after Novobiocin (5 ug/ml) / acrD- 0 min before treatment
358	38.41851112	-65.43440433	acrD- 5 min after Novobiocin (20 ug/ml) / acrD- 0 min before treatment
359	76.89514971	-112.4563397	acrD- 5 min after Novobiocin (50 ug/ml) / acrD- 0 min before treatment
360	47.95224379	7.613215138	acrD- 5 min after Novobiocin (200 ug/ml) / acrD- 0 min before treatment
361	178.7230024	121.9889722	DH5alpha OD 0.2 in LB + Amp pUC expression / DH5alpha OD 0.2 in LB no pUC
362	264.455306	470.1308367	DH5alpha OD 0.5 in LB + Amp pUC expression / DH5alpha OD 0.5 in LB no pUC
363	153.1835216	472.3360842	DH5alpha OD 0.9 in LB + Amp pUC expression / DH5alpha OD 0.9 in LB no pUC
364	245.3637454	5.67198672	MG1655 Stationary phase in LB OD 2.4 T1 / MG1655 genomic DNA
365	273.7616736	-65.41657038	MG1655 Stationary phase in LB OD 2.8 T2 / MG1655 genomic DNA
366	263.3902781	-33.00155107	MG1655 Stationary phase in LB OD 3.1 T3 / MG1655 genomic DNA
367	234.5810393	-9.091237732	MG1655 Stationary phase in LB OD 3.1 T4 (for 20 min) / MG1655 genomic DNA
368	214.4339838	-90.37547684	MG1655 Stationary phase in LB OD 3.1 T5 (for 40 min) / MG1655 genomic DNA
369	181.0423423	-16.72554983	MG1655 Stationary phase in LB OD 3.1 T6 (for 60 min) / MG1655 genomic DNA
370	-153.068291	14.68236161	rraA OD600=1.0 / WT OD600=1.0
371	-87.46270344	29.20491582	rraA OD600=0.3 / WT OD600=0.3
372	-37.48835125	55.72279031	rraA OD600=0.5 / WT OD600=0.5
373	-74.21586396	48.14300139	KSL2009 + pTrc99A-rraA (rraR overexpressing) / KSL2009 control
374	-50.73676789	-122.4346152	KSL2000 Rne depletion / KSL2000 control
375	288.7821855	161.4951985	KSL2009 N-Rne depletion / KSL2009 control
376	-247.3605075	-411.9572436	KSL2000 + pTrc99A-rraA (rraR overexpressing) / KSL2000 control
409	181.5853944	-6.293251617	WT Norfloxacin treated for 5 min / WT Nontreated at 0 min
410	117.854258	76.27920107	(recA-) Norfloxacin treated mutant for 5 min / (recA-) Nontreated mutant at 0 min
411	48.27256981	-54.71324275	(topA-) Norfloxacin treated mutant for 5 min / (topA-) Nontreated mutant at 0 min
412	-0.649600149	56.28421115	(dnaC) Norfloxacin treated mutant for 5 min / (dnaC) Nontreated mutant at 0 min
413	152.2449199	7.042927464	WT Norfloxacin treated for 10 min / WT Nontreated at 0 min
414	169.7002408	31.50912341	(recA-) Norfloxacin treated mutant for 10 min / (recA-) Nontreated mutant at 0 min
415	48.27677058	-47.68493999	(topA-) Norfloxacin treated mutant for 10 min / (topA-) Nontreated mutant at 0 min
416	33.55217965	44.1981272	(dnaC) Norfloxacin treated mutant for 10 min / (dnaC) Nontreated mutant at 0 min
417	168.2366282	-23.06056368	WT Norfloxacin treated for 15 min / WT Nontreated at 0 min
418	240.199282	151.0313754	(recA-) Norfloxacin treated mutant for 15 min / (recA-) Nontreated mutant at 0 min
419	59.89892856	-58.08649644	(topA-) Norfloxacin treated mutant for 15 min / (topA-) Nontreated mutant at 0 min
420	43.72354712	50.61249706	(dnaC) Norfloxacin treated mutant for 15 min / (dnaC) Nontreated mutant at 0 min
421	137.5602929	101.6801788	WT Norfloxacin treated for 20 min / WT Nontreated at 0 min
422	91.35759875	274.3118218	(recA-) Norfloxacin treated mutant for 20 min / (recA-) Nontreated mutant at 0 min
423	64.41196126	-46.02424474	(topA-) Norfloxacin treated mutant for 20 min / (topA-) Nontreated mutant at 0 min
424	68.62026714	95.89361303	(dnaC) Norfloxacin treated mutant for 20 min / (dnaC) Nontreated mutant at 0 min
425	46.17944912	-11.95487269	gyrB 2 min after upshift to 42 C / gyrB before upshift
426	113.7362054	176.9382269	gyrB 5 min after upshift to 42 C / gyrB before upshift
427	113.635606	205.3355988	gyrB 10 min after upshift to 42 C / gyrB before upshift
428	153.0136969	225.8686536	gyrB 20 min after upshift to 42 C / gyrB before upshift
429	122.7834615	120.394347	WT aerobic pH 5.0 / WT aerobic pH 7.0
430	55.65131497	263.855399	WT aerobic pH 8.7 / WT aerobic pH 7.0
431	304.5835258	223.0083751	WT anaerobic pH 5.0 / WT anaerobic pH 7.0
432	138.2156572	15.18312919	WT anaerobic pH 8.5 / WT anaerobic pH 7.0
433	28.54958582	2.286049779	yceP LB glu 24 hr biofilm cells + 0.06% DMF / WT LB glu 24 hr biofilm cells 
434	-54.80158355	60.67370728	LB glu 24 hr biofilm cells + 600uM indole / WT LB glu 24 hr biofilm cells
435	-108.2089425	-46.03587283	trpE LB glu 24 hr biofilm cells / WT LB glu 24 hr biofilm cells
436	94.89802298	-152.9199356	WT LB 24 hr biofilm cells / WT LB glu 24 hr biofilm cells 
437	-140.5702627	-116.1492779	tnaA LB glu 24 hr biofilm cells / WT LB glu 24 hr biofilm cells
438	-13.22306313	-73.00101362	UV Irradiated 50h / Not irradiated
439	-73.96821097	64.52267128	UV Irradiated 1h / Not irradiated
440	176.1679101	23.98116057	UV Irradiated 1h / Not irradiated: dye swap
441	32.7880698	9.693190865	continuous culture 40h / batch culture 40h
442	45.4810631	31.71630861	continuous culture 500h / batch culture 500h
443	23.86126958	89.31906372	WT + arginine(100 ug/ml) / WT in minimal medium
444	354.1320766	33.28351493	argR + arginine(100 ug/ml) / WT in minimal medium
445	40.83259815	86.26399951	Continuous culture no oxygen / 5 min exposure to oxygen
446	49.57120325	128.3890951	Continuous culture no oxygen / 10 min exposure to oxygen
447	34.10369812	69.43038702	Continuous culture no oxygen / 15 min exposure to oxygen
448	107.7793689	62.77037056	Continuous culture no oxygen / 60 min exposure to oxygen
449	148.851334	114.282882	WT at pH 5.5 for 1 min / WT at pH 7.6
450	408.8904785	393.9864264	WT at pH 5.5 for 5 min / WT at pH 7.6
451	421.8106619	256.8345979	WT at pH 5.5 for 10 min / WT at pH 7.6
452	43.13647646	-14.20898458	exponential growth phase + IAA solution 0.5 mM / exponential growth phase
453	31.81820003	-44.21145325	Aerobic wildtype 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture aerobic wildtype control
454	-70.41381361	14.01585288	Aerobic wildtype 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture aerobic wildtype control (dye swap)
455	81.9977274	125.6943113	Anaerobic wildtype 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture anaerobic wildtype control
456	-17.39380689	36.99559852	Anaerobic wildtype 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture anaerobic wildtype control (dye swap)
457	-147.5758768	31.36713736	Anaerobic norR 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture anaerobic wild type 10 uM each NOC-5 and NOC-7 for 5 minutes
458	-98.19682019	-289.1258487	Anaerobic norR 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture anaerobic wild type 10 uM each NOC-5 and NOC-7 for 5 minutes (dye swap)
459	-123.3245893	-236.7312081	Aerobic norR 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture aerobic wild type 10 uM each NOC-5 and NOC-7 for 5 minutes
460	-198.5527461	-480.1328671	Aerobic norR 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture aerobic wild type 10 uM each NOC-5 and NOC-7 for 5 minutes (dye swap)
461	-181.7002733	-61.31442186	Aerobic hmp 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture aerobic wild type 10 uM each NOC-5 and NOC-7 for 5 minutes
462	-156.2246999	-319.4855734	Aerobic hmp 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture aerobic wild type 10 uM each NOC-5 and NOC-7 for 5 minutes (dye swap)
463	145.1133746	70.83705956	cueO + Fe(II) / WT + Fe(II)
464	39.45515144	8.686007843	BL21 (pOri1) (mu=0.39) / BL21 (mu=0.46)
465	38.07007954	22.13027922	BL21 (pOri2) (mu=0.29) / BL21 (mu=0.46)
466	23.08397219	-17.21537191	BL21 (pOri1) (mu=0.20) / BL21 (mu=0.20)
467	55.09501781	-21.70396981	BL21 (pOri2) (mu=0.20) / BL21 (mu=0.20)
468	-27.1490884	24.3521831	TPEN treated / untreated
469	-258.8871486	-86.62124959	TPEN treated / untreated; dye swap
473	-139.6662887	289.9083083	FliA / WT on MOPS glucose
474	369.27365	876.3427668	flhDC / WT on MOPS glucose
475	-108.4121669	-118.689109	FliA overexpression / empty pTet32 control
476	15.7395224	133.514307	ycfR LB glu biofilm culture for 15h / WT LB glu biofilm culture for 15h
477	145.6376976	44.95209358	WT + (HoxEFUYH [hydrogenase] ) / WT
478	-23.5617567	-7.265197649	Overproduced Rsd / control: OD 0.4
479	110.9405293	60.3726233	Overproduced Rsd / control: OD 0.9
480	138.3522677	50.52538796	Overproduced Rsd / control: OD 1.1
481	44.54466931	-9.814897797	Overproduced Rsd / control: Stationary phase
486	257.2200136	86.00815372	WT anaerobic LB 3h / WT anaerobic LB 2h30
487	253.6523894	266.9751294	UTI89 anaerobic LB 3h / UTI89 anaerobic LB 2h30
488	585.3249876	359.2670418	UTI89 anaerobic LB 3h30 / UTI89 anaerobic LB 2h30
489	358.9588526	484.1064419	WT anaerobic LB 3h45 / WT anaerobic LB 2h30
490	778.3791241	568.8391411	UTI89 anaerobic LB 4h / UTI89 anaerobic LB 2h30
491	316.2550337	466.3042048	WT anaerobic LB 4h30 / WT anaerobic LB 2h30
492	763.4167506	826.7224652	WT aerobic LB 5h / WT aerobic LB 2h30
493	702.5989244	469.3992128	UTI89 aerobic LB 5h / UTI89 aerobic LB 2h30
494	430.9487139	427.2905098	UTI89 anaerobic LB 6h / UTI89 anaerobic LB 2h30
495	186.2520366	468.5039927	WT anaerobic LB 6h45 / WT anaerobic LB 2h30
496	644.1796335	814.3150604	WT aerobic LB 8h / WT aerobic LB 2h30
497	597.9340954	796.2194899	WT aerobic LB 12h / WT aerobic LB 2h30
498	663.7806581	406.5456747	UTI89 aerobic LB 12h / UTI89 aerobic LB 2h30
499	659.7893218	858.6751086	WT aerobic LB 18h / WT aerobic LB 2h30
500	686.2253008	369.0357251	UTI89 aerobic LB 8h / UTI89 aerobic LB 2h30
501	663.9394845	600.3835098	UTI89 aerobic LB 19h30 / UTI89 aerobic LB 2h30
502	517.5899217	924.6618834	WT aerobic LB 26h / WT aerobic LB 2h30
503	371.3378709	603.1192375	UTI89 aerobic LB 26h / UTI89 aerobic LB 2h30
504	-124.4319572	6.434886406	UTI89 gnotobiotic cecum 14 day post-inoculation / MG1655 gnotobiotic cecum 14 day post-inoculation
505	50.00558545	36.23595074	rseA / WT (Exp 1)
506	3.642119874	-21.96751509	rseA / WT (Exp 2)
507	-12.276894	20.67770741	rseA / WT (Exp 3)
508	24.77163525	79.27991707	hfq / WT (Exp 1)
509	33.07909409	133.2498165	hfq / WT (Exp 2)
510	4.729147885	-35.74701148	rpoE overexpression 20 min / WT
511	-137.8622364	-404.6021479	Day 1 anaerobic WT / reference
512	-151.6660562	-124.6487853	Day 3 aerobic lon / reference
513	-80.02035109	-127.8347708	Day 1 anaerobic lon / reference
514	-259.769778	-307.4535926	Day 3 aerobic WT / reference
515	-86.70210127	-255.2712664	Day 1 aerobic WT / reference
516	-147.4345929	-427.7982992	Day 3 anaerobic lon / reference
517	24.48771751	-289.2951238	Day 1 aerobic lon / reference
518	-171.8228067	-375.2061258	Day 3 anaerobic WT / reference
519	27.12870766	38.99472002	5 min oxygen depletion / control with oxygen
520	-43.49694819	-37.68907143	10 min oxygen depletion / control with oxygen
521	-133.1131255	-72.83791283	15 min oxygen depletion / control with oxygen
522	-136.5084983	-58.44421065	60 min oxygen depletion / control with oxygen
523	244.7662399	31.90324498	Benzalkonium chloride adapted strain / control
524	318.3048281	1.546586482	Adapted strain with 50 ppm benzalkonium chloride / control
525	56.14452652	-10.85111599	NsrR- phenocopy + TMA + NO2 / control
526	-2.742345951	28.11849854	NsrR- phenocopy / control
527	56.91982512	108.9156985	NsrR+ TMA and NO2 / control
528	-127.7490073	-307.5689294	(dinI+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin
529	-106.0181545	-330.4708486	(dinP+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin
530	-91.88001334	-329.4893302	(lexA+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin
531	-126.1790825	-328.6722705	(lon+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin
532	37.42282642	-35.3836301	(luc+) 0.025ug/ml norfloxacin / (luc+) without norfloxacin
533	-130.3550353	-338.807583	(luc+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin
534	-210.2496134	-399.8248357	(mazF+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin
535	-118.9224354	-364.9448454	(recA+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin
536	-250.5461796	-402.9230155	(relE+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin
537	-112.7444145	-309.3542623	(ruvA+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin
538	-114.5481698	-332.129495	(sulA+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin
539	-99.51936966	-339.934415	(umuD+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin
540	-111.3508663	-318.1527029	(uvrA+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin
541	-194.2699085	-129.1477752	(yebF+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
542	235.3583924	77.62049474	(luc+) 0.075ug/ml norfloxacin / (luc+) without norfloxacin
543	-185.646772	-118.5597572	(zipA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
544	-77.79930563	-46.56734132	(yfjF+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
545	-113.849198	-51.34746939	(bcp+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
546	-139.3515937	-47.05786103	(cpxR+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
547	-104.1416029	-43.72334804	(crcB+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
548	-87.46240405	-55.95591577	(crp+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
549	-83.69973547	-83.0086397	(cspF+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
550	-136.8096458	-134.3370941	(dam+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
551	-149.7856179	-58.68317396	(dnaA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
552	-102.6233616	-85.15744966	(dnaN+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
553	-128.2719757	-91.13629658	(dnaT+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
554	-203.7584233	-166.1152079	(emrR+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
555	-98.80505214	-38.26148195	(era+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
556	-69.65053068	-37.86111286	(fis+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
557	-92.51092636	-2.370369152	(fklB+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
558	-107.9865516	-60.40027477	(folA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
559	-140.4208301	-78.63049587	(galF+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
560	-121.8004901	-77.59247532	(gcvR+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
561	-105.5016711	-85.58161408	(gyrA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
562	-162.8698744	-117.0071241	(gyrI+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
563	-168.4259765	-122.2007685	(hlpA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
564	-166.7679024	-145.8090323	(holD+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
565	-201.9197111	-161.2416778	(hscA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
566	-201.000071	-173.6721007	(IHF+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
567	-76.37970465	-40.58446711	(idrA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
568	-69.25216077	-51.57650243	(mcrB+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
569	-85.73731448	-22.20438745	(mcrC+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
570	-163.8688658	-75.74593468	(menB+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
571	-181.6739442	-103.4047541	(menC+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
572	-171.2346618	-77.36224748	(minD+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
573	-181.7775769	-132.6579476	(minE+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
574	-178.6337949	-145.9650372	(murI+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
575	-406.443637	-273.0856057	(yoeB+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
576	-163.9271258	-155.0470317	(nrdA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
577	-176.288429	-165.7051156	(nrdB+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
578	-122.1839029	-87.17243701	(nupC+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
579	-101.7567378	-10.16248968	(pyrC+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
580	-146.6106452	-82.21726726	(rimI+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
581	-195.4649396	-129.5613593	(rstB+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
582	-120.6785876	-118.8084025	(ruvC+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
583	-193.3804618	-117.8245128	(sbcB+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
584	-188.8667491	-116.440386	(uspA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin
585	15.58478501	-66.86069495	WT with 0.025 ug/ml norfloxacin / WT without norfloxacin
586	-47.01651439	-51.70133722	WT with 0.050 ug/ml norfloxacin / WT without norfloxacin
587	204.9455356	-188.0918445	WT with 0.075 ug/ml norfloxacin / WT without norfloxacin
588	62.00692625	-129.690175	(recA-) / WT
589	-42.26383429	-74.75005859	(recA-) 0.075ug/ml norfloxacin / (recA-) without norfloxacin
590	-19.95873666	-14.07985609	(recA-) 1.0ug/ml norfloxacin / (recA-) without norfloxacin
591	448.4729174	-1.500888098	WT with 1.0 ug/ml norfloxacin / WT without norfloxacin
592	53.16725001	8.006016862	luciferase + 0.025ug/ml norfloxacin / luciferase
593	-2.95417387	45.00271147	WT 12 min after 0.025 ug/ml norfloxacin / WT prior to treatment
594	203.5526083	122.7571659	WT 24 min after 0.025 ug/ml norfloxacin / WT prior to treatment
595	239.3113615	82.93739798	WT untreated cells after 24 min / WT prior to treatment
596	330.9794247	217.1820968	WT 36 min after 0.025 ug/ml norfloxacin / WT prior to treatment
597	290.4930639	227.7857705	WT 48 min after 0.025 ug/ml norfloxacin / WT prior to treatment
598	302.4912627	213.7330126	WT 60 min after 0.025 ug/ml norfloxacin / WT prior to treatment
599	357.1516462	252.7118815	WT untreated cells after 60 min / WT prior to treatment
600	-108.2017243	-87.96692205	(ccdB+) 30 min after induction / (ccdB+) 0 min after induction
601	-112.2379915	28.28759406	(ccdB+) 60 min after induction / (ccdB+) 0 min after induction
602	-37.56757738	117.7240404	(ccdB+) 90 min after induction / (ccdB+) 0 min after induction
603	93.05823881	176.2752076	(ccdB+) 120 min after induction / (ccdB+) 0 min after induction
604	1.688837999	27.42692995	(lacZ+) 30 min after induction / (lacZ+) 0 min after induction
605	167.2836731	82.59514488	(lacZ+) 60 min after induction / (lacZ+) 0 min after induction
606	311.7376928	106.3377616	(lacZ+) 90 min after induction / (lacZ+) 0 min after induction
607	231.6719347	61.88859074	(lacZ+) 120 min after induction / (lacZ+) 0 min after induction
608	-94.08838311	-614.4563641	(lacZ+ recA-) 0 min after induction / (lacZ+) 0 min after induction
609	-46.41002759	30.00687861	(lacZ+ recA-) 30 min after induction / (lacZ+ recA-) 0 min after induction
610	-1.409673685	76.02818201	(lacZ+ recA-) 60 min after induction / (lacZ+ recA-) 0 min after induction
611	33.34397822	153.3635857	(lacZ+ recA-) 90 min after induction / (lacZ+ recA-) 0 min after induction
612	-167.0197419	-715.1021346	(ccdB+ recA-) 0 min after induction / (ccdB+) 0 min after induction
613	-114.4516985	30.18690128	(ccdB+ recA-) 30 min after induction / (ccdB+ recA-) 0 min after induction
614	-71.0731597	270.651989	(ccdB+ recA-) 60 min after induction / (ccdB+ recA-) 0 min after induction
615	-130.0501727	381.0885099	(ccdB+ recA-) 90 min after induction / (ccdB+ recA-) 0 min after induction
616	3.426854685	-493.9067891	(lacZ+) W1863 (lambda-) 0 min after induction / (lacZ+) 0 min after induction
617	26.53490541	2.84162869	(lacZ+) W1863 (lambda-) 30 min after induction / (lacZ+) W1863 (lambda-) 0 min after induction
618	175.8151632	169.8470849	(lacZ+) W1863 (lambda-) 60 min after induction / (lacZ+) W1863 (lambda-) 0 min after induction
619	333.027004	488.5302879	(lacZ+) W1863 (lambda-) 90 min after induction / (lacZ+) W1863 (lambda-) 0 min after induction
620	17.51386827	-560.3485089	(ccdB+) W1863 (lambda-) 0 min after induction / (ccdB+) 0 min after induction
621	59.76655273	63.6217167	(ccdB+) W1863 (lambda-) 30 min after induction / (ccdB+) W1863 (lambda-) 0 min after induction
622	457.4746464	383.9700007	(ccdB+) W1863 (lambda-) 60 min after induction / (ccdB+) 0 min after induction
623	699.631016	559.8829568	(ccdB+) W1863 (lambda-) 90 min after induction / (ccdB+) 0 min after induction
624	115.491964	144.3915795	(lacZ+ recA-) 120 min after induction / (lacZ+ recA-) 0 min after induction
625	-263.0621375	356.7456771	(ccdB+ recA-) 120 min after induction / (ccdB+ recA-) 0 min after induction
626	42.1245707	-36.48676792	EMG2 LB + 0.2% glucose 3h post-incubation / EMG2 LB + 0.2% glucose 2.5h post-incubation
627	57.55419163	-35.32426405	EMG2 LB + 0.2% glucose 3.5h post-incubation / EMG2 LB + 0.2% glucose 2.5h post-incubation
628	146.0730309	-5.065955301	EMG2 LB + 0.2% glucose 4h post-incubation / EMG2 LB + 0.2% glucose 2.5h post-incubation
629	214.5448483	37.97943805	EMG2 LB + 0.2% glucose 4.5h post-incubation / EMG2 LB + 0.2% glucose 2.5h post-incubation
630	301.8317338	444.0039447	EMG2 LB + 0.2% glucose 5h post-incubation / EMG2 LB + 0.2% glucose 2.5h post-incubation
631	466.9867869	427.2564217	EMG2 LB + 0.2% glucose 5.5h post-incubation / EMG2 LB + 0.2% glucose 2.5h post-incubation
632	504.0867333	523.7584931	EMG2 LB + 0.2% glucose 6h post-incubation / EMG2 LB + 0.2% glucose 2.5h post-incubation
633	503.0051268	290.2624542	EMG2 LB + 0.2% glucose 8h post-incubation / EMG2 LB + 0.2% glucose 2.5h post-incubation
634	9.956384784	1.206879385	EMG2 LB + 0.4% glucose 3h post-incubation / EMG2 LB + 0.4% glucose 2.5h post-incubation
635	141.3302419	66.14763326	EMG2 LB + 0.4% glucose 3.5h post-incubation / EMG2 LB + 0.4% glucose 2.5h post-incubation
636	366.6428165	180.266938	EMG2 LB + 0.4% glucose 4h post-incubation / EMG2 LB + 0.4% glucose 2.5h post-incubation
637	371.3360852	333.2342848	EMG2 LB + 0.4% glucose 4.5h post-incubation / EMG2 LB + 0.4% glucose 2.5h post-incubation
638	546.464972	552.9063817	EMG2 LB + 0.4% glucose 5h post-incubation / EMG2 LB + 0.4% glucose 2.5h post-incubation
639	519.7252046	563.07033	EMG2 LB + 0.4% glucose 5.5h post-incubation / EMG2 LB + 0.4% glucose 2.5h post-incubation
640	459.6381116	558.886602	EMG2 LB + 0.4% glucose 6h post-incubation / EMG2 LB + 0.4% glucose 2.5h post-incubation
641	327.8223652	578.1371366	EMG2 LB + 0.4% glucose 8h post-incubation / EMG2 LB + 0.4% glucose 2.5h post-incubation
642	61.73539213	-148.212414	ATCC25404 with pR1drd19 24h in LB / ATCC25404 without R1drd19 24h in LB
643	29.51812319	65.83344825	MG1655 with pR1drd19 24h in M9C glu / MG1655 without pR1drd19 24h in M9C glu
644	199.7745157	286.833209	BW25113 with pR1drd19 24h in LB / BW25113 with pR1drd19 7h in LB
645	16.46054476	68.83963343	BW25113 with pR1drd19 24h in LB / BW25113 without pR1drd19 24h in LB
646	287.5812821	227.8625347	BW25113 with pR1drd19 15h in LB / BW25113 with pR1drd19 7h in LB
647	123.5287346	83.30252894	BW25113 15h in LB / BW25113 7h in LB
648	82.66867536	48.24724	BW25113 24h in LB / BW25113 7h in LB
649	-34.57350429	38.1541341	ymgB / WT biofilm on LB 24 h
650	85.5350584	66.58765663	soxR 2 min paraquat treatment / (soxR) before paraquat treatment
651	-47.91957108	-14.96019882	WT 2 min paraquat treatment / WT before paraquat treatment
652	219.5315503	56.46944028	soxR 4 min paraquat treatment / (soxR) before paraquat treatment
653	64.52712144	-24.43972019	WT 4 min paraquat treatment / WT before paraquat treatment
654	121.9476437	-40.08684965	soxR 6 min paraquat treatment / (soxR) before paraquat treatment
655	36.82700097	-57.83390488	WT 6 min paraquat treatment / WT before paraquat treatment
656	115.3848979	-20.99568218	soxR 8 min paraquat treatment / (soxR) before paraquat treatment
657	74.74949344	-87.86547867	WT 8 min paraquat treatment / WT before paraquat treatment
658	172.2490171	55.66045911	soxR 10 min paraquat treatment / (soxR) before paraquat treatment
659	40.36367712	-124.6774791	WT 10 min paraquat treatment / WT before paraquat treatment
660	-37.68304744	-415.7374506	phoU mutant / WT reference
661	111.5957113	-136.9412803	WT tp1: 780 min / WT tp1: 780 min
662	51.14524392	-86.37725221	WT tp2: 830 min / WT tp1: 780 min
663	48.80903682	-130.5048528	WT tp3: 861 min / WT tp1: 780 min
664	92.03843787	87.96099576	WT tp4: 869 min / WT tp1: 780 min
665	218.5408443	223.4080214	WT tp5: 878 min / WT tp1: 780 min
666	274.493746	228.2209799	WT tp6: 888 min / WT tp1: 780 min
667	263.4743164	144.4601689	WT tp7: 898 min / WT tp1: 780 min
668	211.5872428	14.47900345	WT tp8: 908 min / WT tp1: 780 min
669	159.3025707	-84.34152347	WT tp9: 919 min / WT tp1: 780 min
670	93.62856797	-8.085581207	WT tp10: 929 min / WT tp1: 780 min
671	46.21378	-0.8964461	WT tp11: 939 min / WT tp1: 780 min
672	59.81090829	-90.45721559	WT tp12: 969 min / WT tp1: 780 min
673	103.1459077	-66.08957181	WT tp13: 999 min / WT tp1: 780 min
674	-10.77464909	193.1004392	WT tp14: 1035 min / WT tp1: 780 min
675	156.3042423	259.6236012	WT tp15: 1049 min / WT tp1: 780 min
676	285.9496168	313.41083	WT tp16: 1070 min / WT tp1: 780 min
677	154.7138839	291.4964033	WT tp17: 1089 min / WT tp1: 780 min
678	28.44823623	-54.44154734	rpoS tp1: 120 min / WT tp1: 780 min
679	12.69779615	-71.83760635	rpoS tp2: 150 min / WT tp1: 780 min
680	-79.39916507	81.82144223	rpoS tp3: 160 min / WT tp1: 780 min
681	60.16134173	167.5072472	rpoS tp4: 170 min / WT tp1: 780 min
682	24.37864091	298.6772889	rpoS tp5: 180 min / WT tp1: 780 min
683	130.0368428	149.7367397	rpoS tp6: 190 min / WT tp1: 780 min
684	80.07205503	77.70874167	rpoS tp7: 200 min / WT tp1: 780 min
685	100.9676435	-87.61603405	rpoS tp8: 210 min / WT tp1: 780 min
686	-9.107361054	-0.501398491	rpoS tp9: 220 min / WT tp1: 780 min
687	-25.74447998	-18.28578296	rpoS tp10: 250 min / WT tp1: 780 min
688	-56.66853606	51.58760918	rpoS tp11: 290 min / WT tp1: 780 min
689	-91.93584476	89.90529116	rpoS tp12: 315 min / WT tp1: 780 min
690	-40.04208274	138.2010212	rpoS tp13: 330 min / WT tp1: 780 min
691	321.6314538	-120.9858662	crp tp2: 250 min / WT tp1: 780 min
692	119.5369994	181.881955	crp tp5: 405 min / WT tp1: 780 min
693	203.339672	151.6475022	crp tp6: 420 min / WT tp1: 780 min
694	153.0896546	114.3377928	crp tp7: 450 min / WT tp1: 780 min
695	174.9896074	-31.0741363	relA tp1: 832 min / WT tp1: 780 min
696	98.20319781	9.504046077	relA tp2: 865 min / WT tp1: 780 min
697	46.10028233	5.363958318	relA tp4: 896 min / WT tp1: 780 min
698	166.3162617	59.88361701	relA tp5: 909 min / WT tp1: 780 min
699	225.2453734	69.79347421	relA tp6: 916 min / WT tp1: 780 min
700	224.3980918	146.2311974	relA tp7: 925 min / WT tp1: 780 min
701	272.9801227	203.1426532	relA tp8: 935 min / WT tp1: 780 min
702	199.6512741	150.8440693	relA tp9: 945 min / WT tp1: 780 min
703	52.85427129	192.4690007	relA tp10: 955 min / WT tp1: 780 min
704	53.12896333	104.7252631	relA tp11: 966 min / WT tp1: 780 min
705	0.574586406	-342.962474	"PaeR7I r+m+ pTN9, 0 h / PaeR7I r-m+ pTN11, 0 h"
706	-89.56582222	-25.6596282	"PaeR7I r+m+ pTN9, 1 h / PaeR7I r-m+ pTN11, 1 h; Rep1"
707	86.81705756	-455.2228012	"PaeR7I r+m+ pTN9, 1 h / PaeR7I r-m+ pTN11, 1 h; Rep2"
708	197.7562097	8.54276424	"PaeR7I r+m+ pTN9, 1 h 50 m / PaeR7I r-m+ pTN11, 1 h 50 m"
709	485.990852	449.6310772	"PaeR7I r+m+ pTN9, 3 h / PaeR7I r-m+ pTN11, 3 h"
710	-408.7520055	345.7441342	90 min fis / WT
711	-73.03301609	315.5232491	150 min fis / WT
712	300.945305	185.1509879	240 min fis / WT
713	20.52639338	-70.92677938	360 min fis / WT
727	-21.73357022	-69.18741626	argR +NO / argR untreated (expt 1)
728	-45.96450167	-86.63201397	argR +NO / argR untreated (expt 2)
729	55.07123173	217.890723	WT +serine hydroxamate / WT untreated
730	116.9916163	162.4106662	ArcA +NO / ArcA untreated
731	-0.668730549	-49.74553941	WT +degraded DeaNO / WT untreated
732	12.03950994	23.12465385	iscR +NO / iscR untreated
733	84.51358716	309.7561442	metJ +NO / metJ untreated (expt 1)
734	74.34867012	221.6764789	metJ +NO / metJ untreated (expt 2)
735	32.61796971	186.8703829	norR +NO / norR untreated (expt 1)
736	21.06475242	75.20279412	norR +NO / norR untreated (expt 2)
737	-8.588468006	-15.53235139	nsrR +NO / nsrR untreated
738	72.74908173	77.83452603	nsrR hmpA +NO / nsrR hmpA untreated (expt 1)
739	-17.68433018	366.1771857	nsrR hmpA +NO / nsrR hmpA untreated (expt 2)
740	84.1705811	41.14146294	WT +NO / WT untreated (diff platform)
741	94.19422136	188.9314678	WT +NO / WT untreated
742	32.99729466	221.6100317	WT +NO / WT untreated (dye swap)
743	-32.23170934	82.49475654	WT +met +NO / WT untreated
744	10.87897131	-210.5812203	E. coli NCM3722 + 0.3 M NaCl / E. coli NCM3722 control; 30 degrees
745	-12.15629477	-76.35444352	E. coli NCM3722 + 0.3 M NaCl + 1mM glycine betaine / E. coli NCM3722 control; 30 degrees
746	-164.458661	-160.3816329	E. coli NCM3722 + 0.3 M NaCl / E. coli NCM3722 control; 43 degrees
747	-134.9003266	-56.53421974	E. coli NCM3722 + 0.3 M NaCl + 1mM glycine betaine / E. coli NCM3722 control; 43 degrees
748	-87.67900026	-286.1255589	rpoS biofilm  / WT biofilm
749	-98.97123481	281.7083587	WT biofilm / WT exponential
750	91.06000454	-25.16165007	rpoS exponential / WT exponential
751	423.8003261	915.5620168	WT stationary phase / WT exponential
752	-331.6587787	-563.5599482	rpoS stationary / WT stationary
753	105.3337029	128.1324074	0 min aerobic to anaerobic shift / control
754	-24.52892044	195.8672167	2 min aerobic to anaerobic shift / control
755	35.77876329	215.9780561	5 min aerobic to anaerobic shift / control
756	38.39076519	287.4889642	15 min aerobic to anaerobic shift / control
757	444.6908311	586.0393785	25 min Rep 1 aerobic to anaerobic shift / control
758	397.3176389	681.762939	25 min Rep 2 aerobic to anaerobic shift / control
759	237.076789	482.0324757	35 min aerobic to anaerobic shift / control
760	199.3390193	319.5758626	45 min aerobic to anaerobic shift / control
761	209.7175892	490.8766905	55 min Rep 1 aerobic to anaerobic shift / control
762	298.8987002	547.0718298	55 min Rep 2 aerobic to anaerobic shift / control
763	-210.7507023	-181.5506221	pck overexpression early log phase / WT early log phase
764	-291.6074339	-260.0532544	ppc overexpression early log phase / early log phase
765	-157.8580934	-209.3286729	ppc overexpression chemostat / WT chemostat
766	-137.6823299	-237.9758637	pck overexpression chemostat / WT chemostat
767	-69.98177169	31.0442887	WT +DPTA / WT untreated (expt 1)
768	28.34199767	23.72138023	WT +DPTA / WT untreated (expt 2)
769	-59.5658108	-65.58227553	cysB +500uM GSNO / cysB untreated
770	91.67533431	198.1554568	nsrR +500uM GSNO / nsrR untreated
771	119.1567972	214.7761772	flhDC +500uM GSNO / flhDC untreated (expt 1)
772	8.012566833	70.79405227	WT +met +500uM GSNO / WT +met untreated (expt 2)
773	96.80150353	149.7230278	WT +cys +500uM GSNO / WT +cys untreated
774	81.71043878	196.3693899	flhDC +500uM GSNO / flhDC untreated (expt 2)
775	95.36995665	280.9887999	WT +100uM GSNO / WT untreated
776	80.5189708	210.4616085	WT +100uM GSNO / WT untreated (dye swap)
777	19.47457466	73.66541829	dpp +100uM GSNO / dpp untreated
778	110.6878173	234.9955482	WT +500uM GSNO / WT untreated
779	0.646601513	62.92980339	WT +met +500uM GSNO / WT +met untreated (expt 1)
780	17.19807989	40.7470582	metJ +500uM GSNO / metJ untreated
781	3.934396484	53.07835884	metJ +500uM GSNO / metJ untreated (dye swap)
782	50.26491059	-94.18572495	yncC biofilm cells / wt biofilm cells
783	3.425670082	-41.87869776	yncC colony / wt colony
784	105.9342214	13.47781642	4h LB biofilm hha / WT
785	93.47361213	10.47732815	4h LB-glu biofilm hha / WT
786	40.64442433	-24.27396153	15h LB-glu biofilm hha / WT
787	47.27183921	-28.64654995	24h LB-glu biofilm hha / WT
788	64.60757526	21.64097716	S TP1 / A TP1
789	286.4050624	-195.6720416	L TP1 / A TP1
790	-23.87033771	-265.2955979	S TP2 / A TP2
791	-16.37709694	24.65054872	L TP2 / A TP2
792	35.51392689	36.42307811	S TP3 / A TP3
793	75.75345711	19.0720563	L TP3 / A TP3
794	39.37079549	17.63527135	S TP4 / A TP4
795	92.61056233	10.42070781	L TP4 / A TP4
797	354.4533981	-10.80893841	23 degrees C / 37 degrees C
798	4.483405227	60.04244737	lsrR / W3110 wild-type
799	25.3814908	-1.523424655	lsrK / W3110 wild-type
804	-217.6729488	263.9562351	L-threonine producing strain / W3110 lacI (pKK223-3) control
806	-9.361151262	-12.87815699	luxS in LB / WT W3110 in LB
807	72.3755457	45.28972455	luxS in LB + 0.8% glucose / WT W3110 in LB + 0.8% glucose
824	43.04288174	177.2309283	1% tannin / continuous culture without tannin
825	79.7215268	-227.7049351	rpoS / WT
826	53.49605143	-174.9133684	sdiA free-living cells 30 degrees / WT free-living cells 30 degrees
827	12.96433038	9.650012018	luxS free-living cells +AI-2 30 degrees / luxS free-living cells without AI-2 30 degrees
828	122.4062852	167.9114722	luxS free-living cells +AI-2 37 degrees / luxS free-living cells without AI-2 30 degrees
829	2.534515446	-117.4359629	luxS free-living cells +AI-2 37 degrees / luxS free-living cells without AI-2 37 degrees
830	13.42503284	21.26881756	tnaA biofilm +100 uM indole 30 degrees / tnaA biofilm without indole 30 degrees
831	-90.76398898	-152.273101	tnaA biofilm +100 uM indole 37 degrees / tnaA biofilm without indole 37 degrees
832	120.1357236	-62.96427931	WT biofilm cells 30 degrees / WT free-living cells 30 degrees
833	100.5346133	20.47797713	sdiA with biofilm cells +1mM indole 30 degrees / sdiA biofilm cells without indole 30 degrees
834	41.57328695	-80.44262706	hha overexpression / control
835	-34.24100385	-17.77985083	10 ug cefsulodin -5 min / untreated -5 min
836	-12.40068006	-0.01487709	0.03 ug mecillinam -5 min / untreated -5 min
837	30.05710591	7.102229134	10 ug cefsulodin and 0.03 ug mecillinam -5 min / untreated -5 min
838	-29.13482171	-18.63302813	10 ug cefsulodin 5 min / untreated 5 min
839	7.159627423	-2.064447713	0.03 ug mecillinam 5 min / untreated 5 min
840	42.7521048	14.6623545	10 ug cefsulodin and 0.03 ug mecillinam 5 min / untreated 5 min
841	-67.73550321	-104.2066405	60 ug cefsulodin 5 min / untreated 5 min
842	83.95595694	39.59392222	60 ug cefsulodin 10 min / untreated 10 min
843	65.03938413	71.50237155	10 ug cefsulodin 20 min / untreated 20 min
844	4.73945934	-19.15494879	0.03 ug mecillinam 20 min / untreated 20 min
845	12.03110796	26.44533879	10 ug cefsulodin and 0.03 ug mecillinam 20 min / untreated 20 min
846	-137.4981243	4.780418069	60 ug cefsulodin 20 min / untreated 10 min
847	-32.55003734	-41.17479046	10 ug cefsulodin 40 min / untreated 40 min
848	-9.922438764	25.58493182	0.03 ug mecillinam 40 min / untreated 40 min
849	86.36915925	65.68628783	10 ug cefsulodin and 0.03 ug mecillinam 40 min / untreated 40 min
850	-64.94229288	137.1865718	60 ug cefsulodin and 0.3 ug mecillinam 40 min / untreated 40 min
851	-50.75329073	99.79537633	0.3 ug mecillinam 60 min / untreated 60 min
852	-59.88069805	-120.7858114	batch culture control / (T2) glucose limited fed-batch (dye swap)
853	158.1825376	46.27908375	(T2) glucose limited fed-batch / batch culture control 
854	-107.6424634	-103.1195507	batch culture control / (T3) glucose limited fed-batch (dye swap)
855	102.8962415	64.44432727	(T3) glucose limited fed-batch / batch culture control
856	-60.73773291	-107.9096766	batch culture control / (T4) glucose limited fed-batch (dye swap)
857	135.1469487	43.44374219	(T4) glucose limited fed-batch / batch culture control
858	-64.14039344	-150.6491906	batch culture control / (T5) glucose limited fed-batch (dye swap)
859	58.84363045	96.9209624	(T5) glucose limited fed-batch / batch culture control
860	-54.46846141	-151.2316124	batch culture control / (T6) glucose limited fed-batch (dye swap)
861	119.6768704	106.5498725	(T6) glucose limited fed-batch / batch culture control
862	-86.11234361	-131.1799227	batch culture control / (T7) glucose limited fed-batch (dye swap)
863	107.6327924	69.80898715	(T7) glucose limited fed-batch / batch culture control
864	-55.33904815	-169.3104352	batch culture control / (T8) glucose limited fed-batch (dye swap)
865	172.3121322	64.95832634	(T8) glucose limited fed-batch / batch culture control
866	-9.183530309	-12.15811523	batch culture control / (T1) glucose limited fed-batch (dye swap)
867	5.296436976	9.982067167	(T1) glucose limited fed-batch / batch culture control 
872	90.43807142	29.24721113	MG1655 10 ug bicyclomycin / MG1655 control
873	75.32226564	49.27802024	MG1655 25 ug bicyclomycin / MG1655 control
874	-39.2586034	270.0342886	MG1655 100 ug bicyclomycin / MG1655 control
875	56.36451462	209.1017864	O157:H7 100 ug bicyclomycin / O157:H7 control
876	74.00372202	190.3318354	MDS42 100 ug bicyclomycin / MDS42 control
877	-8.854818987	155.4231465	MDS42 nusA / MDS42 control
878	198.8541883	225.2151285	MDS42 nusG / MDS42 control
907	50.10408928	92.28466621	E. coli B178 groESL(-) expressing human Hsp60 and Hsp10 / E. coli B178 groESL(-) expressing human wt and Val98Ile Hsp60 and Hsp10
908	3.343087819	272.7920931	4.5% NaCl in TSB / pooled RNA control
909	-336.0311209	-115.5188266	15% glycerol in TSB / pooled RNA control
910	28.70939519	63.25956007	HCl (pH 4.75) in TSB / pooled RNA control
911	-309.8048611	47.89527163	NaOH (pH 9.6) in TSB / pooled RNA control
912	-334.6158354	75.86895508	0.05 M acetate in TSB / pooled RNA control
913	-95.73358672	155.5859102	Heat (46o) in TSB / pooled RNA control
914	-176.4459262	193.9359801	5% ethanol in TSB / pooled RNA control
915	33.39230125	110.6674078	Cold (15o) in TSB / pooled RNA control
916	-351.1111892	-77.27382655	7 ppm benzalkonium Cl in TSB / pooled RNA control
917	-372.4732123	-97.2056209	9 ppm benzalkonium Cl in TSB / pooled RNA control
918	-33.07049161	123.9669334	150 mg/ml ethidium Br in TSB / pooled RNA control
925	-79.44088088	400.5655735	relA spoT isoleucine starved / WT replete isoleucine
926	-114.7314137	558.7404789	relA isoleucine starved / WT replete isoleucine
927	716.6896896	1211.913121	WT isoleucine starved / WT replete isoleucine
928	560.8747307	1477.309097	crp isoleucine starved / WT replete isoleucine
929	59.9646135	965.6081997	dksA isoleucine starved / WT replete isoleucine
930	558.7645453	1462.833783	lrp isoleucine starved / WT replete isoleucine
931	431.476355	1188.61491	rpoS isoleucine starved / WT replete isoleucine
932	-285.2101973	-23.29051709	rpoS isoleucine starved / WT isoleucine starved
933	95.42135114	134.0832672	WT isoleucine starved tp 1 / WT replete isoleucine
934	103.9461133	133.2667493	WT isoleucine starved tp 2 / WT replete isoleucine
935	392.6762778	108.5656001	WT isoleucine starved tp 3 / WT replete isoleucine
936	144.1488181	196.5179556	WT isoleucine starved tp 4 / WT replete isoleucine
937	195.3748635	415.6001914	WT isoleucine starved tp 5/ WT replete isoleucine
938	232.6172316	453.2481513	WT isoleucine starved tp 6 / WT replete isoleucine
939	416.1463362	536.5488119	WT isoleucine starved tp 7 / WT replete isoleucine
940	390.1761578	754.0356255	WT isoleucine starved tp 8 / WT replete isoleucine
941	453.391679	892.8746512	WT isoleucine starved tp 9 / WT replete isoleucine
942	492.9171096	1199.391332	WT isoleucine starved tp 10 / WT replete isoleucine
943	621.0439168	1263.687768	WT isoleucine starved tp 11 / WT replete isoleucine
944	636.4992137	1501.357505	WT isoleucine starved tp 12 / WT replete isoleucine
945	746.4947526	492.6505261	WT stationary phase / WT exponential phase
946	84.56455755	42.63843151	hupA / WT LB exponential
947	-99.07351863	-2.361699681	hupA / WT LB transition
948	-43.7428511	45.01810111	hupA / WT LB stationary
949	-60.66485831	87.62028743	hupB / WT LB exponential
950	55.20436995	6.550773954	hupB / WT LB transition
951	126.879061	29.83181574	hupB / WT LB stationary
952	59.3420043	-11.30593227	hupAB / WT LB exponential
953	-171.3066462	-117.8769749	hupAB / WT LB transition
954	-68.26343164	-146.9389792	hupAB / WT LB stationary
955	16.05753431	-49.6543288	rpoS / WT LB exponential
956	-508.8551665	19.08717221	rpoS / WT LB stationary
957	-534.3491326	-263.2680281	hupAB / WT M9 glucose exponential
958	-384.7739655	-137.5635317	hupAB / WT M9 glycerol exponential
959	-42.1151256	91.52183889	hupAB / WT M9 glucose stationary
960	71.07207243	462.8212555	hupAB / WT M9 glycerol stationary
967	-699.4954043	915.7569264	WT 100 mM Cd(II) for 10 min / WT
968	-388.5397155	747.5905022	gshA 100 mM Cd(II) for 10 min / WT
969	-319.8833057	1192.430466	gshB 100 mM Cd(II) for 10 min / WT
970	-657.8598701	-476.6313506	sdiA overexpression / empty vector control
971	-254.0789131	-142.075109	sdiA1E11 overexpression / empty vector control
972	-49.31438544	71.87305913	zinc limited chemostat / control
973	23.48670665	-13.89704734	zinc limited chemostat / control (dye swap)
975	-27.12418479	-39.49752894	mazEF relBEF chpB yefM-yoeB dinJ-yafQ  / MG1655 WT biofilm cells on LB
976	133.7697672	298.375112	15 min oxygen downshift / control
977	84.45183907	576.5417879	45 min oxygen downshift / control
978	278.4933375	767.7885179	75 min oxygen downshift / control
979	45.73541683	166.1063703	sucrose / control on min glucose
980	11.85777718	-19.37921495	NaCl / control on min glucose
986	-96.41020768	82.32959857	5 min no Cd pH 7 / 5 min no Cd pH 5 (dye swap)
989	112.9852268	168.1105443	Generation 50 LB + 10% cranberry juice  / LB
990	70.37463125	222.0782178	Generation 160 LB + 10% cranberry juice / LB
991	-117.7944242	-20.37837762	Generation 210 LB + 10% cranberry juice / LB
992	193.5791448	156.7094586	Generation 230 LB + 10% cranberry juice / LB
993	64.84840856	-43.97942314	yjgK / WT control biofilm
994	-5.102854442	-77.08269593	5FU / control biofilm
995	347.5685805	442.2186239	WT stationary phase / WT exponential phase
996	-100.2346687	-796.2757442	rpoS / WT M63 glucose exponential
997	-213.3345644	122.2973493	rpoS / WT M63 glucose stationary
1004	-160.897457	34.65674111	30 uM CO-RMs 15 min / aerobic control
1005	-221.9112269	-17.03801431	30 uM CO-RMs 15 min / aerobic control (dye swap)
1006	-43.57910814	45.78343123	100 uM CO-RMs 15 min / anaerobic control
1007	-87.55709006	-45.78705792	100 uM CO-RMs 15 min / anaerobic control (dye swap)
1016	-433.7785665	307.2536243	attachment stage biofilm / colony stage biofilm
1017	-453.8197628	12.33460239	attachment stage biofilm / maturation stage biofilm
1018	-418.9122273	-88.61581333	attachment stage biofilm /planktonic exponential phase
1019	16.70834029	-395.8961219	colony stage biofilm /planktonic exponential phase
1020	37.69834697	-100.9685513	maturation stage biofilm /planktonic exponential phase
1021	515.4524853	-2070.806452	planktonic exponential phase  / planktonic stationary phase
1022	69.4215129	525.8526523	wildtype 1% isobutanol / wildtype
1023	34.04375898	503.5775417	wildtype 1% butanol / wildtype
1024	138.2132424	437.9796945	wildtype 3% ethanol / wildtype
1025	143.1453752	715.5837302	ihfA 1% isobutanol / ihfA
1026	135.4518561	340.0825894	fur 1% isobutanol / fur
1027	355.1475687	606.9419277	phoB 1% isobutanol / phoB
1028	283.835202	582.018121	arcA 1% isobutanol / arcA
1029	272.6592404	552.9805863	ubiE1% isobutanol / ubiE
1032	616.5437306	-358.5327373	biofilm outside / biofilm inside
1033	-754.2567959	-1402.68153	Planktonic exponential phase  / Planktonic stationary phase
1034	288.345813	-202.7342013	biofilm inside  / Planktonic exponential phase
1035	-14.19263619	111.2976403	biofilm outside / Planktonic exponential phase
1036	-76.27503287	2.497552694	rpoS- / WT
1037	63.95255069	464.8837765	evolved rpoS+ (DMS1735) / WT
1038	144.1940493	95.85301347	evolved rpoS+ (DMS1737) / WT
1039	274.8117793	199.8769	evolved rpoS+ (DMS1739) / WT
1040	-12.18394845	85.69916328	evolved rpoS+ (DMS1741) / WT
1041	194.0984348	240.7187234	evolved rpoS+ (DMS1743) / WT
1042	-134.3118239	27.39561263	evolved rpoS- (DMS1745) / rpoS- (DMS1688)
1043	-10.0123737	-33.65660045	evolved rpoS- (DMS1747) / rpoS- (DMS1688)
1044	-223.1730103	-184.7791248	evolved rpoS- (DMS1749) / rpoS- (DMS1688)
1045	-104.0154797	-63.35208175	evolved rpoS- (DMS1751) / rpoS- (DMS1688)
1046	-0.115611381	-16.42107519	evolved rpoS- (DMS1753) / rpoS- (DMS1688)
1047	66.37575241	-51.05444867	"TOM-Green/IsoILR1/GSHI, cis-DCE / non-cloned genes, cis-DCE"
1048	101.9508558	28.22463818	"TOM-Green/EchA F108L/I219L/C248I, cis-DCE / TOM-Green, cis-DCE"
1049	261.1809874	360.5920536	"BW25113, H2O2 / BW25113, water"
1050	319.9973761	92.06561446	"BW25113 ygiW, H2O2 / BW25113 ygiW, water"
1051	192.0583477	307.1139908	"BW25113 ychH, H2O2 / BW25113 ychH, water"
1052	-177.6784127	-144.439315	UV irradiation (50 J/m2) / unirradiated
1053	-95.08188139	-158.9767779	FhlA133 (mutated) / FhlA (control)
1054	-5.935514293	-98.31871538	CORM-2 treated_anaerobic / anaerobic control
1055	-54.73698481	151.2636949	CORM-2 treated_aerobic / aerobic control
1056	-254.2463117	-202.4034799	BW25113 ompA/pCA24N ompA  /  BW25113 ompA/pCA24N control
1057	1.657887834	29.35369378	ompA / wt (polystyrene biofilm)
1058	-62.77699504	55.6325863	ompA / wt (glasswool biofilm)
1062	54.11334552	71.31756042	BW25113-mqsR / control
1063	182.6856226	-20.42901995	BW25113/pCA24N-mqsR / control (IPTG)
1064	-65.37081474	7.017493068	BW25113/pCA24N-mqsR / control (IPTG for 15 min)
1065	-174.9960667	320.5666956	"BW25113/pCA24N-mqsR / control (DNA, IPTG)"
1066	113.2519622	105.2757355	"BW25113/pBAD-mqsA / control (DNA, IPTG)"
1070	-133.6900742	-130.6066624	CP4-57-deficient  / wild type
1078	-426.5480501	-938.3809319	triclosan / control
1080	323.8605776	36.49804102	wt GraL / wt control (short term)
1081	-153.8588844	261.8168526	ppGpp0 GraL / ppGpp0 control (short term)
1082	85.78182104	10.23656572	wt GraL / wt control (long term)
1083	168.1056212	-87.4924956	ppGpp0 GraL / ppGpp0 control (long term)
1084	36.13611383	54.74175832	adenosine
1085	-3.399572468	-9.342488108	alanine
1086	48.57590517	61.9462047	arginine
1087	45.15540042	71.27036276	aspartate
1088	71.0882731	121.22817	cysteine
1089	-42.9184889	-20.05947547	cytidine
1090	16.50738931	32.23120077	glutamate
1091	-41.50366497	-13.67605843	glutamine
1092	17.86237556	-30.47096404	glycine
1093	63.26016242	62.02679778	guanosine
1094	18.16448002	49.39882998	histidine
1095	53.88900493	130.5024382	isoleucine
1096	0.788953235	29.92433068	lysine
1097	-52.58649134	-59.41280646	methionine
1098	18.55790082	65.66581489	phenylalanine
1099	-25.82578562	-99.25223857	proline
1100	5.392240976	72.71800764	serine
1101	-1.013907397	-9.784935895	threonine
1102	-18.00437053	18.75751359	thymidine
1103	46.27383217	-14.86199902	tryptophan
1104	-52.15761255	-48.28643031	uridine
1105	32.62321661	-8.144687581	valine
1106	-22.69061248	3.713381227	del27 / WT
1107	-28.75193937	83.1489379	eBOP42 / WT
1108	-14.17142826	87.94120709	eBOP43 / WT
1113	195.1164038	511.3702779	heat shock 45 degrees 10 min / WT log phase
1114	917.8263433	993.0215976	stationary phase / log phase
1115	436.0429758	591.9364576	WT nitrogen-limited medium log phase / WT complete medium log phase
1132	87.36031057	-45.98311101	ada vs. wildtype
1133	119.6520638	-28.899096	wt + MMS  / wt - MMS ( .5 h )
1134	135.9792372	-44.24962356	wt + MMS / wt - MMS ( 1.5 h )
1135	248.593142	-312.196725	wt + MMS / wt - MMS ( 3.9 h )
1136	1270.493575	-796.7921375	ada + MMS / ada - MMS ( .5 h )
1137	-84.08143199	-67.27232982	ada + MMS / ada - MMS ( 1.5 h )
1138	130.473254	-167.7034769	ada + MMS / ada - MMS ( 3.9 h )
1140	-56.8933702	-116.5876897	"0 min, butanol / unstressed"
1141	95.81226576	200.7666667	"30 min, butanol / unstressed"
1142	39.11192954	-65.72021651	"80 min, butanol / unstressed"
1143	43.92876149	-13.72833918	"195 min, butanol / unstressed"
1151	208.2472726	232.4219421	NTG-treated  / control ( - triclosan)
1152	283.83958	268.5825087	NTG-treated / control ( + triclosan)
1155	-10.64211313	-58.40845377	Recombinant T1 / Recombinant T0
1156	-147.0322095	51.29621703	Recombinant T4 / Recombinant T0
1157	-116.6333157	114.7737617	Recombinant T1 + IPTG / Recombinant T0
1158	-171.4902416	93.21929912	Recombinant T4 + IPTG / Recombinant T0
1159	-46.35493541	-63.39238844	wt T1 / wt T0
1160	-8.071759786	-103.6208335	wt T4 / wt T0
1161	-34.20609683	-62.32188198	wt T1 + IPTG / wt T0
1162	-34.61324807	-59.40675025	wt  T4 + IPTG / wt T0
1163	95.68918912	6.852789296	serine hydroxamate T1  / recombinant T0
1164	-111.5545362	68.55840763	Heat-Shocked 15 min / Recombinant T0
1165	-206.8402405	21.02888595	Heat-Shocked 15 min + IPTG / Recombinant T0
1171	466.5632378	43.43055695	Crp* + Glucose / WT + Glucose
1172	317.4164876	119.4165492	Crp* / WT
1173	260.186086	392.5160763	LY180 + furfural / LY180
1174	175.9608392	264.3675182	EMFR9 + furfural / EMFR9
1175	-22.47822137	-44.70656922	LY180 del yqhC / LY180
1176	36.81155064	50.54736212	LY180   furfural / LY180
1177	74.33994218	55.12645683	LY180 del yqhC   furfural / LY180 del yqhC
1178	10.98742906	-33.19315098	LY180 del yqhC   furfural / LY180   furfural
1179	-913.2711675	-704.5097956	"E. coli DST160, tolerant to high succinic acid concentration / E. coli W3110 WT"
1181	-139.0998858	-170.3961621	Biofilm / Planktonic
1182	-68.21602707	-105.0344602	CHIR-090 / DMSO control
1183	-289.5868861	-89.20685391	hfq deletion / wt
1184	-384.9116893	-97.95391551	mgrR - / wt
1185	-1.913464011	79.76921667	plasmid mgrR / plasmid control
1186	-10.43309573	-35.51823541	peroxynitrite / control
1187	-32.59706243	-46.79185146	hydrogen peroxide / control
1188	-43.30091492	-145.8864817	pFnrS / plasmid control
1189	-452.0966194	-641.4304953	Wild-type Cells / pooled reference RNA
1190	-68.53053453	1598.58309	SHX-treated WT / pooled reference RNA
1191	-183.1446816	114.0357784	Delta dksA Cells / pooled reference RNA
1192	-823.8771838	741.196427	SHX-treated Delta dksA Cells / pooled reference RNA
1193	-204.7253073	47.09539619	reuterin / control
1195	-315.7863179	427.4796206	thymine limited - 15 / control - 0
1196	-188.645564	438.4432078	thymine limited - 30 / control - 0
1197	109.7303623	-127.9250945	thymine limited - 45 / control - 0
1198	75.33764027	14.91521028	thymine limited - 60 / control - 0
1199	-8.598248464	100.4694555	thymine limited - 90 / control - 0
1200	-59.94706791	84.79315892	thymineless - 15 / control - 0
1201	-1.412257569	193.3037504	thymineless - 30 / control - 0
1202	-106.1304456	225.7986122	thymineless - 45 / control - 0
1203	23.41636285	179.4444367	thymineless - 60 / control - 0
1204	157.4331397	50.34347403	thymineless - 90 / control - 0
1206	-115.4098601	-45.22024012	rpoS mutants / WT
1207	41.36303318	91.79823215	rpoN mutants / WT
1208	7.702095658	-12.34533878	cold stress T1 / control T1
1209	-85.85257029	-80.73108429	cold stress T2 / control T2
1210	-234.2490017	-365.1446237	cold stress T3 / control T3
1211	-379.8046509	-449.6877047	cold stress T4 / control T4
1212	-367.2024961	-519.5725982	cold stress T5 / control T5
1213	-402.8734109	-518.9400253	cold stress T6 / control T6
1214	-460.3872095	-506.4105301	cold stress T7 / control T7
1215	-143.7560894	153.1933572	cold stress T8 / control T8
1216	31.48078536	14.62691649	heat stress T1 / control T1
1217	-43.34697921	-33.26745889	heat stress T2 / control T2
1218	201.5348548	1138.049667	heat stress T3 / control T3
1219	213.408196	1136.303617	heat stress T4 / control T4
1220	394.3451992	1327.497364	heat stress T5 / control T5
1221	289.8396966	1287.521646	heat stress T6 / control T6
1222	355.2057264	465.5586675	heat stress T7 / control T7
1223	281.7208994	1308.609892	heat stress T8 / control T8
1224	74.12892673	29.78290734	oxidative stress T1 / control T1
1225	-3.340867269	-91.20903664	oxidative stress T2 / control T2
1226	160.0411821	-23.52548218	oxidative stress T3 / control T3
1227	264.7614664	540.3957334	oxidative stress T4 / control T4
1228	283.2513332	597.17187	oxidative stress T5 / control T5
1229	119.3884496	532.4119404	oxidative stress T6 / control T6
1230	180.1082031	612.7279219	oxidative stress T7 / control T7
1231	175.1571584	1.058127709	oxidative stress T8 / control T8
1232	384.6181167	276.9104989	glucose-lactose shift T2 / control T2
1233	435.6910593	635.1155324	glucose-lactose shift T3 / control T3
1234	556.4354932	745.6232243	glucose-lactose shift T4 / control T4
1235	1415.752786	984.3172646	glucose-lactose shift T5 / control T5
1236	1285.120652	746.9339445	glucose-lactose shift T6 / control T6
1237	1380.645043	728.7481727	glucose-lactose shift T7 / control T7
1238	-27.06385658	-0.429898531	NADH Oxidase / Reference
1239	-18.94865112	-0.04269437	ATPase / Reference
1252	179.8403958	123.2326777	EHEC DMEM QseD / EHEC DMEM WT
1253	-147.5200929	-1024.592987	K-12 DMEM QseD / K-12 DMEM WT
1254	-117.9042807	-922.1903397	K-12 LB QseD / K-12 LB WT
1255	-73.71291834	-184.2559331	luxS deletion / WT
1256	63.13621628	-158.7923648	HG228 / MG1655
1257	31.46318704	58.57030819	E. coli mutant aerobic / WT anaerobic
1258	46.48687996	46.06670049	E. coli mutant  aerobic / WT aerobic
1259	145.7670994	274.2481298	clpV deleted mutant / Wild Type
1260	61.15938462	261.1149424	hcp deleted mutant / Wild Type
1261	136.0935643	555.2237778	icmF deleted mutant / Wild Type
1262	69.70841653	-359.0245544	ldhA pflB mutated / wild type
1263	-19.58735604	-8.648685445	nusA11 mutant / WT
1264	23.49534463	21.41887505	T2 exposed norfloxacin and indole / T0 exposed norfloxacin
1265	31.61576787	10.10152624	T3 reexposed norfloxacin / T0 exposed norfloxacin
1273	116.9066722	29.65176171	ptsN mutant / WT
1282	185.4189951	-57.82395737	"pSpoT / pBRplac ,control"
1283	-15.80078171	406.6166086	MG1655star on glucose  / WT on glucose
1284	8.321405207	477.7268397	flhD on glucose / WT on glucose
1285	-14.49242153	422.3636777	MG1655star on mannose / WT on mannose
1286	70.19769785	486.3595364	flhD on mannose / WT on mannose
1287	79.59916719	421.8272054	MG1655star A600=0.2 mucus / WT A600=0.2 mucus
1288	139.5544592	448.6938282	flhD A600=0.2 mucus / WT A600=0.2 mucus
1289	118.4057793	296.2318642	MG1655star A600=0.5 mucus / WT A600=0.5 mucus
1290	62.68793301	345.5168137	flhD A600=0.5 mucus / WT A600=0.5 mucus
log2.fold_change._Fis_vs_WT	-268.016653	296.4652179	NA
log2.fold_change._Hns_vs_WT	868.7947732	-33.49080172	NA
log2FoldChangeExpAEV	2449.470935	1710.602904	NA
log2FoldChangeExpAmA	3153.922882	3269.821278	NA
log2FoldChangeExpBEV	1789.531576	1328.903086	NA
log2FoldChangeExpBmB	2147.029308	2381.501652	NA
log2FoldChangemAEV	-790.1277049	-1628.193389	NA
log2FoldChangemBEV	-447.2407192	-1122.355884	NA
log2FoldChangeStatAEV	1718.775852	1473.102744	NA
log2FoldChangeStatAmA	2079.785165	3244.872511	NA
log2FoldChangeStatBEV.x	816.0334867	993.0031713	NA
log2FoldChangeStatBEV.y	816.0334867	993.0031713	NA
log2FoldChangeStatBmB	1158.303466	1553.216592	NA
wt.on_ko.on_log2_fold_change	4.656480971	-77.69773189	NA