Prediction of highly expressed genes in microbes based on chromatin accessibility

Willenbrock, Hanni; Ussery, David W

doi:10.1186/1471-2199-8-11

BMC Molecular Biology

Table 1 Predicted highly expressed non-translated E. coli genes by the position preference measure.

From: Prediction of highly expressed genes in microbes based on chromatin accessibility

Gene	bnumber	Type	Gene expression rank	PP	Gene	bnumber	Type	Gene expression rank	PP
asnT	b1977	tRNA	122	0.1076	leuP	b4369	tRNA	404	0.1294
asnW	b1984	tRNA	121	0.1076	selC	b3658	tRNA	617	0.1295
asnU	b1986	tRNA	101	0.1076	thrT	b3979	tRNA	143	0.1300
asnV	b1989	tRNA	127	0.1076	serW	b0883	tRNA	196	0.1310
thrV	b3273	tRNA	898	0.1154	rrsH	b0201	Ribosomal and stable RNAs	15	0.1318
valW	b1666	tRNA	1544	0.1172	rrsA	b3851	Ribosomal and stable RNAs	1	0.1318
valT	b0744	tRNA	114	0.1212	tyrU	b3977	tRNA	172	0.1318
valZ	b0746	tRNA	130	0.1212	rrsG	b2591	Ribosomal and stable RNAs	6	0.1319
valX	b2402	tRNA	124	0.1212	rrsC	b3756	Ribosomal and stable RNAs	2	0.1320
valY	b2403	tRNA	109	0.1212	rnpB	b3123	misc_RNA	73	0.1332
aspU	b0206	tRNA	219	0.1215	leuZ	b1909	tRNA	920	0.1338
aspV	b0216	tRNA	233	0.1215	rrfF	b3272	Ribosomal and stable RNAs	14	0.1338
aspT	b3760	tRNA	150	0.1215	rrlH	b0204	Ribosomal and stable RNAs	4	0.1348
serU	b1975	tRNA	1420	0.1221	metU	b0666	tRNA	309	0.1351
leuU	b3174	tRNA	3814	0.1229	metT	b0673	tRNA	229	0.1351
valV	b1665	tRNA	2022	0.1233	rrlA	b3854	Ribosomal and stable RNAs	12	0.1351
thrU	b3976	tRNA	66	0.1235	rrlC	b3758	Ribosomal and stable RNAs	18	0.1352
ileU	b3277	tRNA	274	0.1239	rrlE	b4009	Ribosomal and stable RNAs	5	0.1352
ileT	b3852	tRNA	236	0.1239	rrlG	b2589	Ribosomal and stable RNAs	3	0.1354
argQ	b2691	tRNA	455	0.1241	rrlD	b3275	Ribosomal and stable RNAs	30	0.1355
argZ	b2692	tRNA	765	0.1241	lysT	b0743	tRNA	123	0.1357
argV	b2694	tRNA	401	0.1241	lysW	b0745	tRNA	142	0.1357
ffs	b0455	misc_RNA	686	0.1255	lysY	b0747	tRNA	94	0.1357
trpT	b3761	tRNA	1483	0.1276	lysZ	b0748	tRNA	131	0.1357
pheV	b2967	tRNA	3047	0.1285	lysQ	b0749	tRNA	113	0.1357
pheU	b4134	tRNA	1995	0.1285	dicF	b1574	RNA; Cell division	3004	0.1361
leuT	b3798	tRNA	171	0.1287	proK	b3545	tRNA	3076	0.1367
leuQ	b4370	tRNA	502	0.1287

These 55 non-translated genes are among the 10% genes with lowest PP values (listed from lowest to highest PP values). The 39 genes highlighted in bold are also found to be highly expressed according to microarray gene expression levels and their rank are shown according to the measured microarray gene expression level (from highest to lowest, low rank => highly expressed).

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ISSN: 1471-2199

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