Correlations between log2 based expression ratios from transcriptomic and proteomic studies at exponential phase (ethanol-treated cell at 10 h versus control cells at 6 h).

a: The direction of comparison; 1: from significant protein list to identify their corresponding genes for correlation; 2: from significant gene list to identify their corresponding proteins for correlation; 3: both the proteins and their corresponding genes used for correlation calculation have same statistical significant differential expression level, and the results of comparisons are same from either directions. P: proteomics, A: transcriptomics; S: statistically significant, 1.5: at least 1.5-fold difference; 2.0: at least 2-fold difference. The numbers for proteomic and transcriptomic studies before comparison are: P: 942; SP: 95 (94 proteins with corresponding gene expression were used for SP); SP1.5: 84; SP2.0: 61; A: 1694; SA: 912; SA1.5: 174; SA2.0: 48. Number: the number of gene-protein pairs after comparison; Correlation: the R-squared number between the log2 based expression ratio (ethanol-treated cell versus control cells) of proteins identified from proteomics and log2 based expression ratio (ethanol-treated cell versus control cells) of genes identified from microarray. →: the direction for comparison; For example, P→A is to identify the corresponding genes in microarray data from the protein list of proteomic data. SP1.5→A is to identify the corresponding genes in microarray data from the protein list of proteomic data with at least 1.5-fold changes.### 比较方向（a）说明： 1. 从显著蛋白质列表中鉴定其对应基因以开展相关性分析； 2. 从显著基因列表中鉴定其对应蛋白质以开展相关性分析； 3. 用于相关性计算的蛋白质及其对应基因均具备相同的统计学显著性差异表达水平，且两种比较方向所得结果完全一致。 缩写定义：P 代表蛋白质组学（proteomics），A 代表转录组学（transcriptomics）；S 代表具有统计学显著性；1.5 表示至少1.5倍表达差异；2.0 表示至少2倍表达差异。 比较前蛋白质组学与转录组学研究的特征数量如下： P：942；SP：95（其中94个带有对应基因表达数据的蛋白质被用于SP分析）；SP1.5：84；SP2.0：61；A：1694；SA：912；SA1.5：174；SA2.0：48。 指标定义： - Number：比较后得到的基因-蛋白质对的数量； - Correlation：蛋白质组学鉴定的蛋白质的基于log₂的表达比值（乙醇处理细胞与对照细胞的比值），与基因芯片（microarray）鉴定的基因的基于log₂的表达比值（乙醇处理细胞与对照细胞的比值）之间的决定系数（R-squared）。 → 表示比较方向；例如，P→A 指从蛋白质组学数据的蛋白质列表中，在转录组学数据中鉴定对应的基因；SP1.5→A 指从具备至少1.5倍表达变化的蛋白质组学数据的蛋白质列表中，在转录组学数据中鉴定对应的基因。