Our data show that the metabolic changes observed upon overexpression of three of the four genes, AAD10, AAD14 and BAT1, were very significantly aligned with the changes that were predicted from the alignment of transcriptome and metabolome data alone.
We performed the same analysis on Oak BESs significantly aligned with A. thaliana sequences in Swissprot.
Among the 1,823 oak BESs significantly aligned with A. thaliana sequences in Swissprot, 799 BESs were associated with at least one GO term (Additional file 8).
For DAV and for T. assigna virus, respectively, no block and one block could be significantly aligned with a probability < 0.01.
Where the results of local HER2 status were discordant with those of HERmark, as in the two discordant groups, the OS curves were significantly aligned with those of HERmark results, but not with the local HER2 status.
While 839 ESTs were rejected for being too small (< 60 nucleotides) or displaying very low complexity, 447 additional FcB1-ESTs could be significantly aligned with loci on the P. falciparum genome (3D7), revealing 24 additional clusters.
The SNP number was further reduced to 4,341 after filtering the SNPs residing in the fragments which were significantly aligned with repetitive sequences http://phaseolus.genomics.purdue.edu/data/pv_gba_recon_repeats.fasta (269 SNPs).
The SNPs residing in the fragments which were significantly aligned with common bean repetitive sequences http://phaseolus.genomics.purdue.edu/data/pv_gba_recon_repeats.fasta or with bacterial sequences deposited in GenBank, as identified with the Megablast software with W = 30, were also eliminated.
Each structurally annotated yeast membrane protein in our final data set is associated with its most significantly aligned orthologs in the three closely related yeasts S. paradoxus, S. mikatae, and S. bayanus, as determined from orthology and sequence annotations in the Fungal Orthogroups Repository (Wapinski et al. 2007).
