Table 2. SEED subsystems that are significantly enriched in cDNA data sets relative to DNA data sets (0.98 confidence level, based on the method described in Rodriguez-Brito et al., 2006).

Depth	Subsystema	Representation in cDNA(%)	Representation in DNA(%)
25 m	Ammonia_assimilation	1.52	0.25
	Photosystem_I	1.72	0.58
	Proteorhodopsin	1.00	0.03
	Ribosome_LSU_bacterial	3.04	1.23
	Ribosome_SSU_bacterial	2.58	0.79
	Universal_GTPases (mostly elongation factors)	2.36	1.31
	RNA_polymerase_bacterial	2.46	1.25
	Transcription_initiation,_bacterial_sigma_factors	0.80	0.21
	Terminal_cytochrome_c_oxidases	1.60	0.38
	Ubiquinone_menaquinone–cytochrome_c_reductase_complexes	0.58	0.11
	Oxidative_stress	0.90	0.28
75 m	Ammonia_assimilation	1.09	0.26
	Photosystem_I	2.38	0.66
	Photosystem_II	2.31	0.81
	Proteorhodopsin	0.80	0.03
	Ribosome_LSU_bacterial	2.90	1.20
	Ribosome_SSU_bacterial	1.97	0.79
125 m	CO2_uptake,_carboxysome	1.20	0.49
	Peptidoglycan_biosynthesis	2.28	1.24
	Chlorophyll_biosynthesis	2.34	0.87
	Photosystem_I	5.24	0.37
	Photosystem_II	5.21	0.46
	Proteorhodopsin	1.34	0.04
	Ribosome_LSU_bacterial	3.92	1.32
	Ribosome_SSU_bacterial	2.69	0.77
	Universal_GTPases (mostly elongation factors)	3.05	1.37
	F0F1-type_ATP_synthase	2.14	0.92
	Cytochrome_B6-F_complex	0.86	0.16
	Transport_of_Iron	1.78	0.40
500 m	Peptidoglycan_biosynthesis	4.63	1.12
	Ammonia_assimilation	3.43	0.12
	Ribosome_SSU_bacterial	1.41	0.67
	Terminal_cytochrome_c_oxidases	1.55	0.51

^aSignificantly enriched in cDNA samples at the 0.98 confidence level.