Additional file 19: Table S5. of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

Ribosome density calculations and comparisons. Sheet 1. Ribosome densities in procyclic forms. The average number of ribosomes per ORF was calculated as follows. First, we needed to correct the ribosome profiling results for the gene copy number in the genome assembly, since during the initial alignments, the reads had been spread out among all orthologues. Orthologue counts were taken from TritrypDB. Unexpected numbers were checked against our previous read alignment data [20], and in some cases manually. Read results for some gene families (such as amino acid transporters) are unreliable because related genes show different regulation. The orthologue counts used are in column D. All RPM were multiplied by the orthologue count (column H). Numbers of mRNAs per cell [16] were previously calculated assuming a total of 19,000 non-VSG mRNAs in bloodstream forms, and 43,000 non-EP-procyclin mRNAs/cell in procyclics [17]. There are about 275000 ribosomes per procyclic parasite and 125000 per bloodstream form [17]. The ribosome densities are calculated using these numbers. In practice, the densities are likely to be lower. About 5 % of ribosomes are likely to be on ORFs that were excluded from the analysis (Procyclin, VSG, ESAGs, and from repetitive elements). Approximately 70 % of all ribosomal RNA is in polysomes, 20 % is in monosomes and the rest is in subunits (our unpublished results); we do not know what proportion of the ribosomes in the monosomal fraction is engaged in translation. Sheet 2. Ribosome densities in bloodstream forms. Sheet 3. Ribosome densities and half-lives in procyclic forms, using only the “reliable” values that were chosen for modelling. Sheet 4. Ribosome densities and half-lives in bloodstream forms, using only the “reliable” values that were chosen for modelling. (XLSX 2688 kb)核糖体密度计算与对比。工作表1：前循环型（procyclic forms）中的核糖体密度。每个开放阅读框（Open Reading Frame, ORF）的平均核糖体数目计算方法如下：首先，需针对基因组组装中的基因拷贝数对核糖体谱分析（ribosome profiling）结果进行校正，因初始比对阶段中测序读段会分散至所有直系同源基因（orthologues）中。直系同源基因计数取自TriTrypDB。异常数值将与本团队此前的测序读段比对数据[20]进行核对，部分数值还需人工校正。部分基因家族（如氨基酸转运蛋白家族）的测序结果不可靠，因其相关基因存在不同调控模式。本次使用的直系同源基因计数位于D列。所有每百万读段数（Reads Per Million, RPM）均乘以直系同源基因计数（H列）。每细胞信使RNA（messenger RNA, mRNA）数目[16]此前已通过以下假设计算得到：血流型（bloodstream forms）中总共有19000条非可变表面糖蛋白（Variant Surface Glycoprotein, VSG）mRNA，前循环型中每细胞含43000条非EP-前循环蛋白（EP-procyclin）mRNA[17]。每个前循环型寄生虫约含275000个核糖体，每个血流型寄生虫约含125000个核糖体[17]。核糖体密度即基于上述数值计算得到。实际情况中该密度大概率偏低：约5%的核糖体位于本次分析排除的开放阅读框区域（包括前循环蛋白、VSG、ESAGs以及重复序列元件）。约70%的核糖体RNA位于多核糖体（polysomes）中，20%位于单核糖体（monosomes）中，剩余部分以核糖体亚基形式存在（本研究未发表结果）；目前尚不明确单核糖体组分中有多大比例的核糖体参与翻译过程。工作表2：血流型中的核糖体密度。工作表3：仅选用建模所需“可靠”数值得到的前循环型核糖体密度与半衰期（half-lives）。工作表4：仅选用建模所需“可靠”数值得到的血流型核糖体密度与半衰期。（XLSX格式，文件大小2688 KB）