In heart failure reactivation of RNA-binding protein function results in expression of thousands of fetal-specific isoforms

Table S3: Differential gene expression analysis Shown is the differential expression analysis between: iPSC-derived cardiovascular progenitor cells (iPSC-CVPC) and adult heart; iPSC-CVPC and adult arteria; adult heart and adult arteria. For each gene, we report: gene ID; gene name; the tested tissues (tissue 1 and tissue 2); effect size, standard error, p-value and FDR correction (Bonferroni). Effect size &gt; 0 corresponds to genes where the expression in tissue 1 is greater than tissue 2.<br>Table S4: Functional enrichment analysis (genes) The table shows the functional enrichment analysis for genes differentially expressed between each pair of CVS tissues (Table S3). For each gene set, we report: the tested tissues (tissue 1 and tissue 2); the gene set collection, as defined by MSigDB, the gene set name and its URL; the number of tested genes in the gene set; the average effect size for all the tested genes in the gene set and for all the other expressed genes; p-value (t-test); and FDR (Benjamini-Hochberg).<br>Table S5: Differential isoform expression analysis Shown is the differential isoform expression analysis between: iPSC-CVPC and adult heart; iPSC-CVPC and adult arteria; adult heart and adult arteria. For each isoform, we report: isoform ID, gene ID, gene name; the tested tissues (tissue 1 and tissue 2); effect size, standard error, p-value and FDR correction (Bonferroni); mean isoform use in each of the two tested tissues and the log₂ ratio between them; whether the isoform is differentially expressed (FDR &lt; 0.05). Effect size &gt; 0 corresponds to isoforms where the expression in tissue 1 is greater than tissue 2.<br>Table S6: Functional enrichment analysis (isoforms) The table shows the functional enrichment analysis of genes that have at least one CVS tissue-specific isoform, compared with genes that do not have differentially expressed isoforms between each pair of CVS tissues (Table S5). For each gene set, we report: the tested tissues (tissue 1 and tissue 2); the gene set collection, as defined by MSigDB, the gene set name and its URL; the number of tested genes in the gene set; the enrichment calculated using the <i>estimate</i> parameter in the <i>fisher.test</i> function in R; p-value (Fisher’s exact test); and FDR (Benjamini-Hochberg).<br>Table S13: Differential gene expression analysis (cell types) Shown are the associations between the expression of each expressed gene and isoform and cell type proportions in all bulk RNA-seq CVS samples. For each gene and isoform, we report: isoform ID, gene ID, gene name; the cell type whose proportion is tested for association with expression; effect size, standard error, p-value, FDR correction (Bonferroni); whether the expression of the gene or isoform is associated with cell type proportion (FDR &lt; 0.05 and effect size &gt; 0).<br>Table S14: Functional enrichment analysis (cell types) The table shows the functional enrichment analysis for genes associated with each cell type. The table is organized as Table S4, with a difference: cell type, rather than “tissue 1” and “tissue 2” is reported. For each cell type, we determined the association (effect size) between its proportion and the expression of each gene, and used the effect sizes of all expressed genes as input for gene set enrichment analysis (GSEA). We observed that the most significantly enriched gene sets corresponded to the main function associated with each cell type, including mitochondrial and cell respiration functions for cardiac muscle, immune response for immune cells, cytoskeleton and actin binding for smooth muscle.<br>Table S15: Differential gene and isoform expression using cell type proportions as covariates Shown is the differential expression analysis for both genes and isoforms performed using ridge regression and cell type proportions as covariates between: iPSC-CVPC and adult heart; iPSC-CVPC and adult arteria; adult heart and adult arteria. For each gene and isoform, we report: isoform ID, gene ID and gene name; the tested tissues (tissue 1 and tissue 2); the covariate, including “tissue”, which represents the differential expression between tissue 1 and tissue 2, and each of the cell types; effect size, standard error, p-value and FDR correction (Bonferroni).<br>Table S18: Differential expression between heart failure and healthy CVS tissues The table shows the results from differential expression analysis of genes and isoforms between pre-LVAD samples and the three healthy CVS tissues (iPSC-CVPC, adult heart and adult arteria). Columns A-D show gene and transcript information, including: transcript ID, gene ID, gene name, and analysis type (gene or isoform). Columns E-F show the pairs of tested tissues. Columns G-J show the effect size, its standard error, p-value and FDR correction (Bonferroni’s method). FDR correction was performed independently on genes and isoforms.表S3：差异基因表达分析。本表格展示了以下组别间的差异表达分析：诱导多能干细胞衍生的心血管祖细胞（iPSC-derived cardiovascular progenitor cells，以下简称iPSC-CVPC）与成人心脏组织；iPSC-CVPC与成人动脉组织；成人心脏组织与成人动脉组织。针对每个基因，我们报告以下信息：基因ID、基因名称、检测的两组组织（组织1与组织2）、效应量、标准误、p值以及邦费罗尼（Bonferroni）校正后的错误发现率（False Discovery Rate，FDR）。效应量>0代表组织1中的基因表达量高于组织2。 表S4：基因功能富集分析。本表格展示了每一组心血管系统（cardiovascular system, CVS）组织间差异表达基因的功能富集分析（对应表S3）。针对每个基因集，我们报告以下信息：检测的两组组织（组织1与组织2）、由分子特征数据库（Molecular Signatures Database，MSigDB）定义的基因集集合、基因集名称及其链接；基因集中的检测基因数量；该基因集内所有检测基因以及其余所有表达基因的平均效应量；p值（t检验）以及本杰明-霍赫贝格（Benjamini-Hochberg）校正后的FDR。 表S5：差异异构体表达分析。本表格展示了以下组别间的差异异构体表达分析：iPSC-CVPC与成人心脏组织；iPSC-CVPC与成人动脉组织；成人心脏组织与成人动脉组织。针对每个异构体，我们报告以下信息：异构体ID、基因ID、基因名称；检测的两组组织（组织1与组织2）；效应量、标准误、p值以及邦费罗尼校正后的FDR；两种检测组织中的异构体平均使用率及其二者间的log₂比值；该异构体是否存在差异表达（FDR<0.05）。效应量>0代表组织1中的异构体表达量高于组织2。 表S6：异构体功能富集分析。本表格展示了针对至少携带一种心血管系统（CVS）组织特异性异构体的基因，与不存在每一组CVS组织间差异表达异构体的基因的比较分析（对应表S5）的功能富集分析。针对每个基因集，我们报告以下信息：检测的两组组织（组织1与组织2）、MSigDB定义的基因集集合、基因集名称及其链接；基因集中的检测基因数量；通过R语言fisher.test函数中estimate参数计算得到的富集得分；p值（费希尔精确检验）以及本杰明-霍赫贝格校正后的FDR。 表S13：（细胞类型）差异基因表达分析。本表格展示了所有批量RNA测序（bulk RNA-seq）的CVS样本中，每个表达基因与异构体的表达量与细胞类型占比之间的关联。针对每个基因与异构体，我们报告以下信息：异构体ID、基因ID、基因名称；与表达量关联检测的细胞类型；效应量、标准误、p值以及邦费罗尼校正后的FDR；该基因或异构体的表达量是否与细胞类型占比存在关联（FDR<0.05且效应量>0）。 表S14：（细胞类型）功能富集分析。本表格展示了与每种细胞类型存在关联的基因的功能富集分析。本表格结构与表S4一致，区别在于：此处报告的是细胞类型，而非“组织1”与“组织2”。针对每种细胞类型，我们先确定其占比与每个基因表达量之间的关联（效应量），并将所有表达基因的效应量作为输入进行基因集富集分析（Gene Set Enrichment Analysis，GSEA）。本研究观察到，最显著富集的基因集对应每种细胞类型的核心功能，包括心肌细胞的线粒体与细胞呼吸功能、免疫细胞的免疫应答功能、平滑肌细胞的细胞骨架与肌动蛋白结合功能。 表S15：以细胞类型占比为协变量的差异基因与异构体表达分析。本表格展示了以岭回归（ridge regression）分析、以细胞类型占比为协变量，在以下组别间进行的基因与异构体差异表达分析：iPSC-CVPC与成人心脏组织；iPSC-CVPC与成人动脉组织；成人心脏组织与成人动脉组织。针对每个基因与异构体，我们报告以下信息：异构体ID、基因ID与基因名称；检测的两组组织（组织1与组织2）；协变量，包括代表组织1与组织2间差异表达的“组织”项，以及每种细胞类型；效应量、标准误、p值以及邦费罗尼校正后的FDR。 表S18：心力衰竭与健康CVS组织间的差异表达分析。本表格展示了左心室辅助装置（Left Ventricular Assist Device，LVAD）植入前样本与三种健康CVS组织（iPSC-CVPC、成人心脏组织与成人动脉组织）间的基因与异构体差异表达分析结果。A-D列展示基因与转录本信息，包括：转录本ID、基因ID、基因名称以及分析类型（基因或异构体）。E-F列展示检测的组织配对信息。G-J列展示效应量、其标准误、p值以及邦费罗尼（Bonferroni’s method）校正后的FDR。FDR校正分别针对基因与异构体独立进行。