Analyzing stochastic transcription to elucidate the nucleoid's organization

BMC Genomics

Table 1 The spectral analyses of the autocorrelations

Data set A (active transcription)						Data set B (stochastic transcription)
pSymA (set A)			rnd pSymA (set A)			pSymA (set B)			rnd pSymA (set B)
No of Periods	Period	Amplitude	No of Periods	Period	Amplitude	No of Periods	Period	Amplitude	No of Periods	Period	Amplitude
1	1294.000	0.584	23	56.261	0.028	12	107.833	0.040	615	2.104	0.051
12	107.833	0.158	341	3.795	0.026	6	215.667	0.022	371	3.488	0.021
6	215.667	0.081	563	2.298	0.024	70	18.486	0.020	566	2.286	0.018
7	184.857	0.077	118	10.966	0.019	47	27.532	0.018	296	4.372	0.017
21	61.619	0.050	262	4.939	0.019	43	30.093	0.017	393	3.293	0.015
43	30.093	0.048	640	2.022	0.016	107	12.093	0.016	99	13.071	0.015
3	431.333	0.042	248	5.218	0.014	238	5.437	0.016	541	2.392	0.014
70	18.486	0.039	380	3.405	0.014	134	9.657	0.016	430	3.009	0.013
47	27.532	0.036	212	6.104	0.014	9	143.778	0.015	278	4.655	0.013
2	647.000	0.033	39	33.179	0.013	50	25.880	0.015	584	2.216	0.013
8	161.750	0.032	637	2.031	0.013	424	3.052	0.014	610	2.121	0.013
166	7.795	0.025	635	2.038	0.013	48	26.958	0.014	537	2.410	0.013
82	15.780	0.025	21	61.619	0.011	10	129.400	0.013	249	5.197	0.012
5	258.800	0.025	325	3.982	0.011	144	8.986	0.013	407	3.179	0.012
17	76.118	0.023	301	4.299	0.011	2	647.000	0.013	317	4.082	0.011
4	323.500	0.022	636	2.035	0.010	220	5.882	0.012	168	7.702	0.011
30	43.133	0.022	141	9.177	0.009	524	2.469	0.011	386	3.352	0.011
42	30.810	0.017	589	2.197	0.009	53	24.415	0.011	18	71.889	0.010
29	44.621	0.016	318	4.069	0.009	138	9.377	0.011	238	5.437	0.010
11	117.636	0.016	339	3.817	0.009	171	7.567	0.011	471	2.747	0.010

The table shows the spectral analyses for the averaged auto-correlations of pSymA (pSymA) and of pSymA with the genes' positions randomly permutated (rnd pSymA) for data set A and set B. Shown are the first twenty periods with the highest amplitudes, in descending order and the number of periods contained on the replicon. The two spectra of the "real" plasmid are made up of short and long periods. Both have, for example, periods of 108 and 206 genes. The random permutations, however, have only very short periods. The amplitudes for pSymA in set B are lower compared to the set A, as we are looking at a random phenomenon, which is necessarily weaker than active transcription. "No of periods": how many periods can be fitted along the replicon in question.

ISSN: 1471-2164