Genes identified by RNA-Seq as SoxR-dependent in stationary phasea.

aGenes are organized in decreasing order of SoxR-dependence as determined by RNA-Seq.bRNA for this comparison was obtained from 3-day old WT or ΔsoxR cultures, both of which were blue-pigmented.cRNA for this comparison was obtained from 3-day old WT (blue-pigmented) or 1-day old WT (unpigmented) cultures.dFalse discovery rate adjusted q-values were calculated according to the Benjamini-Hochberg procedure [27].ePredicted functions of genes were obtained from StrepDB (http://strepdb.Streptomyces.org.uk).fConfirmed SoxR-targets that are directly regulated by SoxR in response to Act production [5], [6].gThese genes are unlikely to be Act-dependent since they were not differentially expressed between 3-day old versus 1-day old WT samples, and were not considered for further analysis.hSCO1697 is soxR which is constitutively expressed over the course of development, and is not autoregulated [5].Genes identified by RNA-Seq as SoxR-dependent in stationary phasea.

a. 基因按照SoxR依赖性由高到低排序，该排序通过RNA测序（RNA-Seq）确定。
b. 本对比实验所用RNA取自3日龄野生型（WT）或ΔsoxR菌株培养物，两类培养物均产生蓝色色素。
c. 本对比实验所用RNA取自3日龄野生型（产蓝色色素）或1日龄野生型（无色素）菌株培养物。
d. 经错误发现率校正的q值根据本杰明尼-霍赫贝格法（Benjamini-Hochberg procedure）[27]计算得到。
e. 基因的预测功能信息取自StrepDB数据库（http://strepdb.Streptomyces.org.uk）。
f. 经证实的SoxR靶基因可在Act产生过程中受SoxR直接调控[5,6]。
g. 此类基因不太可能受Act调控，因其在3日龄与1日龄野生型样本中未出现差异表达，故未纳入后续分析。
h. SCO1697即为soxR基因，其在发育过程中呈组成型表达，且不存在自我调控现象[5]。
经RNA测序鉴定的稳定期SoxR依赖性基因。