Abstract：
Large-scale transcriptomic data are crucial for understanding the molecular features of hepatocellular carcinoma (HCC). Integrated 15 transcriptomic datasets of HCC clinical samples, the first version of HCC database (HCCDB v1.0) was released in 2018. Through the meta-analysis of differentially expressed genes and prognosis-related genes across multiple datasets, it provides a systematic view of the altered biological processes and the inter-patient heterogeneities of HCC with high reproducibility and robustness. With four years having passed, the database now needs integration of recently published datasets. Furthermore, the latest single-cell and spatial transcriptomics have provided a great opportunity to decipher complex gene expression variations at the cellular level with spatial architecture. Here, we present HCCDB v2.0, an updated version that combines bulk, single-cell, and spatial transcriptomic data of HCC clinical samples. It dramatically expands the bulk sample size by adding 1656 new samples from 11 datasets to the existing 3917 samples, thereby enhancing the reliability of transcriptomic meta-analysis. A total of 182,832 cells and 69,352 spatial spots are added to the single-cell and spatial transcriptomics sections, respectively. A novel single-cell level and 2-dimension (sc-2D) metric is proposed as well to summarize cell type-specific and dysregulated gene expression patterns. Results are all graphically visualized in our online portal, allowing users to easily retrieve data through a user-friendly interface and navigate between different views. With extensive clinical phenotypes and transcriptomic data in the database, we show two applications for identifying prognosis-associated cells and tumor microenvironment. HCCDB v2.0 is available at http://lifeome.net/database/hccdb2.
摘要：
大规模转录组数据对于理解肝细胞癌（HCC）的分子特征至关重要。肝癌临床样本的综合15个转录组数据集，HCC数据库的第一个版本(HCCDBv1.0)于2018年发布.通过对多个数据集的差异表达基因和预后相关基因的荟萃分析，它提供了HCC的改变的生物过程和患者间异质性的系统视图，具有高度的可重复性和鲁棒性。四年过去了，数据库现在需要集成最近发布的数据集。此外，最新的单细胞和空间转录组学为破译具有空间结构的细胞水平的复杂基因表达变异提供了很好的机会。这里,我们介绍了HCCDBv2.0，这是一个结合了批量的更新版本，单细胞,和HCC临床样本的空间转录组数据。通过将11个数据集中的1656个新样本添加到现有的3917个样本中，极大地扩展了批量样本大小，从而提高转录组荟萃分析的可靠性。总共182,832个细胞和69,352个空间点被添加到单细胞和空间转录组学切片中，分别。还提出了一种新颖的单细胞水平和二维（sc-2D）度量标准，以总结细胞类型特异性和失调的基因表达模式。结果在我们的在线门户中都以图形方式可视化，允许用户通过用户友好的界面轻松检索数据，并在不同的视图之间导航。数据库中有大量的临床表型和转录组数据，我们展示了鉴定预后相关细胞和肿瘤微环境的两种应用。HCCDBv2.0可在http://lifeome.net/database/hccdb2查阅。
