The bench scientist's guide to statistical analysis of RNA-Seq data

BMC Research Notes

Table 2 Functional category significance of optimized and marginally significant genes

Functional Category	Optimized		DESeq marginal		edgeR marginal
	# of genes	p-value	# of genes	p-value	# of genes	p-value
Stress	497	0 *	70	2.20E-03 *	19	0.17
Signaling	909	0 *	102	0.43	40	0.70
Cell wall	263	8.51E-29 *	28	0.14	4	0.50
Photosynthesis	117	3.79E-05 *	22	0.76	4	0.23
RNA	1132	6.04E-05 *	222	0.01 *	98	4.40E-03 *
Hormone metabolism	321	3.08E-04 *	36	0.01 *	19	0.51
DNA	133	0.002 *	34	0.70	19	0.03 *
Major CHO metabolism	76	0.003 *	5	0.72	7	0.42
Lipid metabolism	223	0.023 *	23	0.34	16	0.88
Mitochondrial electron transport / ATP synthesis	71	0.042 *	2	0.17	10	0.04 *
TCA cycle	44	0.049 *	---	---	7	0.53

The genes eliminated from Step C in Figure 1 are grouped into functional categories and compared with the final optimized list of significant genes. p-value indicates the significance that transcript abundance of all the genes within a specified category are changing in a similar manner compared to all other categories. Asterisks signify p-value below p = 0.05.

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