A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes

BMC Genomics

Table 1 Comparison of the six algorithms, using the microarray hybridization data from the MG1655 sequenced strain. The result of using each algorithm were compared to BLASTN data and are shown below.

	Cut-off	TP	FP	TN	FN	Sensitivity	Specificity	M-Score
	0.50	4231	3	1452	58	98.65	99.78	98.90
	0.33	4244	6	1449	45	98.95	99.59	99.11
Naïve	0.25	4249	10	1445	40	99.07	99.31	99.12
Cut-off	0.20	4253	20	1435	36	99.16	98.63	99.02
	0.10	4265	125	1330	24	99.44	91.40	97.41
GENCOM*		4203	3	1452	86	97.99	99.79	98.45
GACK**	EPP = 50	4116	1	1554	173	95.97	99.93	96.97
	EPP= 0	4202	3	1452	87	97.97	99.79	98.43
Porwollik		4219	2	1453	70	98.37	99.86	98.75
MKD***		4243	12	1443	46	98.93	99.18	98.99
Mixture	Bimodal	4256	20	1435	33	99.23	98.63	99.07
	Trimodal	4236	4	1451	53	98.76	99.73	99.01

The number of genes estimated as correctly conserved (True positives, TP), genes identified as conserved but actually are variable (false positives, FP), genes identified as correctly variable (true negatives TN), and genes identified falsely as variable (false negative FN), are given. The sensitivity, specificity, and M-Score are also calculated, where the sensitivity = TP/(TP+FP), specificity = TN/(FP+TN), and M-Score = Sensitivity*prevalence + Specificity*(1-prevalence)
* Institute of Food Research method (GENCOM)
** Genotyping Analysis by Charlie Kim method (GACK)
*** Minimum Kernel Density method (MKD)

ISSN: 1471-2164