Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software

Table 1 Comparison among different methods used for transcriptome reconstruction

		ORA (SOLiD)	Cufflinks (SOLiD)	Tiling arrays	5’-RACE	Illumina
5’-UTRs
ORA (SOLiD)	45 g/l ^	-	nd*	(1753/2473) 71% *	(446/615) 72% *	(1712/2298) 75% *	6 g/l*
Cufflinks (SOLiD)		nd ^	-	(1836/2903) 63% *	(586/885) 66% *	(1750/2656) 66% *
Tiling arrays		(860/1336) 64% ^	(1882/3149) 60% ^	-	(1039/1281) 81% *	(3092/4180) 74% *
5’-RACE		(488/721) 68% ^	(572/974) 59% ^	(1039/1281) 81% ^	-	(786/1009) 78% *
Illumina		(1784/2739) 65% ^	(1599/2906) 55% ^	(3092/4180) 74% ^	(786/1009) 78% ^	-
3’-UTRs
ORA (SOLiD)	45 g/l ^	-	nd*	(1125/2473) 45% *	nd *	(1348/2527) 53% *	6 g/l*
Cufflinks (SOLiD)		nd ^	-	(1293/2903) 45% *	nd *	(1356/2923) 46% *
Tiling arrays		(643/1336) 48% ^	(1491/3149) 47% ^	-	nd *	(2774/4551) 61% *
5’-RACE		nd ^	nd ^	nd ^	-	nd *
Illumina		(1609/3040) 53% ^	(1621/3214) 50% ^	(2774/4551) 61% ^	nd ^	-

Percentages of 5’-UTRs and 3’-UTRs regions determined using different methods and software and having length differences of < = 50 bases. For each comparison, the number of UTR regions with a length difference of < = 50 bases and the total number of UTRs identified with both methods are shown in parenthesis. “SOLiD ORA” refers to the transcripts determined from our experiment using ORA, “Tiling arrays” refers to the data reported by Xu and colleagues [10], “5’-RACE” and “Illumina sequencing” refers to data reported by Nagalakshmi and colleagues [9] and “SOLiD Cufflinks” refers to the transcripts reported in our experiments and analyzed using Cufflinks [20]. In the top-right half of both matrices are reported 6 g/l results (marked using * symbol), in the bottom-left half of both matrices are reported 45 g/l results (marked using ^ symbol).

ISSN: 1471-2164