Pathway analysis of the transcriptome and metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms

Table 2 Overview of the different filtering steps applied to the list of significant transcripts and the gene universe

Filter number applied	f0	f1	f2	f3	f4	f5
Number of significant transcripts	4557	4305	4080	3568	2379 (2672*)	2246 (2503*)
Size of gene universe	61413	30887	29343	26118	18326	14254

* including transcripts interrogated by probe sets constructed from P. × canescens sequences that were higher expressed in P. euphratica, and transcripts interrogated by probe sets constructed from P. euphratica sequences that were higher expressed in P. × canescens
f0 = raw list: Raw lists are the list of significant genes as calculated by SAM and all probe sets on the microarray; f1 = probe set ID present/absent: filter f1 removed probe sets identified as absent by the MAS 5.0 algorithm; f2 = probe set SD: filter f2 removed probe sets with SD in the upper 5% quantile; f3 = annotation available: filter f3 removed probe sets without annotation; f4: species of origin of probe set: filter f4 removed probes sets biased due to the poplar species used for their construction; f5 = duplicate gene models: filter f5 removed duplicate gene models.

ISSN: 1471-2229