The largest string of same-direction genes, consisting of 391 genes, was found on the complementary strand of Leishmania infantum chromosome 31 (NC_009415); there were only two genes in the forward direction (Supplementary Table S3).
In addition, by combining our previous results on reconstruction of TRNs on oxidative stress, iron imbalance stress, and acid stress with this study, we could make a list of genes consisting of entire sets of gene products regulated by corresponding 8 different TFs in response to these four different environmental stresses (Supplementary Data 2).
For these PCR fragment-based microarrays, called Sm6kPCR, a collection of probes for the 6207 predicted protein-coding genes consisting of 6046 gene-specific PCR fragments and 161 70 mer oligonucleotides was arrayed in high density on glass slides.
The chloroplast genomes of P. chekiangensis and P. bournei identically contain 112 genes consisting of 78 protein coding genes, 30 tRNA genes, and 4 rRNA genes, with the size of 152,849 and 152,853 bp, respectively.
Genes consisting of fewer than 30 codons and those containing overlaps were eliminated.
Genes consisting of fewer than 33 aa were eliminated, and those containing overlaps were manually evaluated.
Hsf1 forms a homotrimer and recognizes heat shock elements (HSEs) in promoters of target genes consisting of at least three inverted repeats of nGAAn.
Os11g0569701 was the most common gene structure (141 genes), consisting of 2 exons and an intron, which inserted the GAA or GAG codon between G-A in the PK domain.
Eight time-course expression profiles were simulated with the mean expression profiles graphed in Figure 2. In total, 800 genes consisting of 100 genes per cluster were simulated with 40 equally spaced time points.
The studies of the effects of these mutations on viability, when each strain was grown in rich medium, have identified a set of essential genes, consisting of about 20% of all the genes [1].
A database of resistances genes was created from (1) all sequences in Antibiotic Resistance Database (ARDB) [48] and (2) sequences from known quinolone resistance genes consisting of sequences from qnrA-D, qnrS, qepA, acrA-B, norA-C and oqxA-B [29], [32], [49].
