Transcript and protein profiling identify candidate gene sets of potential adaptive significance in New Zealand Pachycladon

Table 2 Numbers of up-regulated transcripts and proteins in P. cheesemanii, P. exile and P. novae-zelandiae

	CH up	CH down	CH up	CH up
	EX+NZ down	EX+NZ up	EX down	NZ down
T	371	74	69	936
P	124	173	60	141
	EX up	EX down	EX up	EX up
	CH+NZ down	CH+NZ up	CH down	NZ down
T	134	70	45	946
P	109	136	161	110
	NZ up	NZ down	NZ up	NZ up
	CH+EX down	CH+EX up	CH down	EX down
T	305	1184	221	297
P	321	109	359	211

Expression of transcripts (T) and proteins (P) in each species (P. cheesemanii, CH, P. exile, EX, P. novae-zelandiae, NZ) was compared with expression in the remaining two species combined (6 group comparisons) and separately (6 pairwise comparisons). For example, 371 transcripts and 124 proteins were up-regulated in CH when compared with EX and NZ combined and 74 transcripts and 173 proteins were down-regulated in CH when compared with EX and NZ combined. Sixty nine transcripts and 60 proteins were up-regulated in CH when compared only to EX and 936 transcripts and 141 proteins were up-regulated in CH when compared only to NZ. The total numbers of transcripts and proteins investigated by microarray analysis and shotgun proteomics were 9601 and 1489, respectively. Locus IDs, gene descriptions, logarithmized expression ratios and adjusted p-values of differentially expressed transcripts and proteins for each of the 12 comparison are compiled in additional file 1, table S1.

ISSN: 2730-7182