Our microarray results demonstrated that at least 127 genes were differentially expressed in the bvrR mutant.
Our microarray results demonstrated several genes directly involved in cell envelope or outer membrane biogenesis differentially expressed in the bvrR mutant.
In this respect, our inability to validate some of our discordant microarray results demonstrates that clearly other factors exist.
Previous experiments reversed microarray results, demonstrating that MpkA negatively regulates genes involved in siderophore production, indicating that many genes involved in iron depletion response are up-regulated in the Δ mpkA mutant strain (e.g. sidA or sidD) [ 8].
Similarly, our microarray results demonstrated a 2.8-fold increase in transcript level of X-linked G glucose-6-phosphate dehydrogenase (G6pdx), an enzyme involved in the first step of pentose phosphate pathway (PPP).
Nonetheless, microarray results demonstrated slight downregulation of TLR2, TLR4, TLR5, and TLR8, together with slight upregulation of MyD88, a key adaptor for these TLRs [ 82], in CD16+ compared to CD16- Mo We demonstrated increased expression of RARA mRNA in CD16+ compared to CD16- Mo.
Collectively, gene ontology and pathway enrichment analyses of microarray and QPCR results demonstrate that arsenic perturbs genes and networks that are involved in the immune response during vertebrate development.
Although the microarray assay results demonstrated more HrpL-downregulated genes than those upregulated by HrpL (Table 1, 2; Supplementary Fig. S2), none of the HrpL-downregulated genes had a hrp box HMM prediction with a high confidence level (Table 2; Supplementary Table S4; Supplementary Fig. S2H-I).
These results demonstrate that the microarray data are reliable.
These results demonstrate that our microarray is a useful tool for analysing the cassava transcriptome and that it is applicable for various cassava genotypes.
