Additional file 5 of Up-regulation of apoptotic- and cell survival-related gene pathways following exposures of western corn rootworm to B. thuringiensis crystalline pesticidal proteins in transgenic maize roots

Additional file 5: Supplementary Table S4. Transcripts with significant differences in read counts (expression) between Diabrotica virgifera virgifera larvae feeding on transgenic maize expressing the insecticidal B. thuringiensis (Bt) Gpp34/Tpp35Ab1 toxin (T5; Table 2) compared to control non-Bt maize (T7). For each transcript, indication of differential expression also being shared when larvae were exposed to Heterorhabditis bacteriophora (Hb) and Metarhizium anisopliae (MA) is indicated with a “1”. Standard output are shown for DESeq2 (baseMean = the average of the normalized counts taken over all samples; log2FoldChange = log2 fold change between the groups; lfcSE = standard error of the log2FoldChange; stat = Wald statistic; pvalue = Wald test P-value; BH_padj = Benjamini-Hochberg adjusted P-value) and EdgeR (logFC = log2 fold change between the groups; logCPM = the average log2-counts-per-million; PValue = the two-sided P-value; BF_FDR = Bonferroni adjusted P-value). Lack of significance for any given transcript in DESeq2 or EdgeR results shown as “-”. The 1374 transcripts differentially expressed in both DESeq2 and EdgeR estimates are shown above the horizonal line. Transcript annotations include presence (Y) or absence (N) of signal_peptide probability (signalp_prob) threshold of > 0.700 shown only for “complete” proteins (match length = 1.0 to Drosophila melanogaster (Dm) or Trobiolium castaneum (Tc) protein models). PFAMSCAN_PfamA search results (format transcript query start, transcript query end: frame, strand (+ or -), range of hit to PFAM domain/PFAM domain name/ E-value/percent identity). Predicted protein information given (transcript start: transcript end: frame: strand (+ or -): amino acid sequence). BLASTx query results to indicated databases shown in standard output format with “/” indicating no values for queries receiving of hits. The 13 transcripts in blue italicized text are putatively derived from Hb or Ma.

附加文件5：补充表S4。本表格收录了取食表达苏云金芽孢杆菌（Bacillus thuringiensis, Bt）Gpp34/Tpp35Ab1毒素的转基因玉米（T5组，见表2）的西方玉米根萤叶甲（Diabrotica virgifera virgifera）幼虫，与取食非Bt转基因对照玉米（T7组）的幼虫之间，读长计数（基因表达量）存在显著差异的转录本。对于每个转录本，若其差异表达特征在幼虫分别暴露于嗜菌异小杆线虫（Heterorhabditis bacteriophora, Hb）和金龟子绿僵菌（Metarhizium anisopliae, MA）时也存在，则以"1"标注。表格展示了DESeq2的标准输出结果：baseMean为所有样本归一化计数的平均值；log2FoldChange为组间log2倍变化倍数；lfcSE为log2FoldChange的标准误；stat为Wald统计量；pvalue为Wald检验P值；BH_padj为Benjamini-Hochberg校正后的P值。同时展示了EdgeR的标准输出结果：logFC为组间log2倍变化倍数；logCPM为平均log2计数每百万；PValue为双侧P值；BF_FDR为Bonferroni校正后的P值。若某转录本在DESeq2或EdgeR分析中无显著性差异，则以"-"标注。在水平线上方展示了同时通过DESeq2和EdgeR分析鉴定出的1374个差异表达转录本。转录本注释信息包括：仅针对"完整"蛋白（匹配长度与黑腹果蝇（Drosophila melanogaster, Dm）或Trobiolium castaneum（Tc）蛋白模型的匹配长度为1.0），是否存在大于0.700的信号肽概率（signalp_prob），以"Y"表示存在，"N"表示不存在。PFAMSCAN_PfamA搜索结果格式为：转录本查询起始位置:转录本查询终止位置:读码框, 链(+或-), PFAM结构域命中区间/PFAM结构域名称/E值/序列一致性百分比。同时提供了预测蛋白信息：转录本起始位置:转录本终止位置:读码框:链(+或-):氨基酸序列。以标准输出格式展示了针对指定数据库的BLASTx查询结果，若查询无命中结果，则以"/"表示对应字段无值。以蓝色斜体标注的13个转录本推测来源于Hb或MA。