NR0B2 regulation during Primary Sclerosing Cholangitis defines a metabolic and pre-malignant reprogramming of Cholangiocyte

Supplemental tables associated to manuscript: Supplemental Table 1. Text mining of the 525 ranked genes found in PUBMED with symptom keywords: this Table describes the 525 ranked genes obtained by text mining with the ‘Génie’ algorithm against the three MESH terms: biliary inflammation, biliary fibrosis and biliary stasis. The respective ranks, p-values and PMID identifiers collected for each gene and each MESH term are presented. Supplemental Table 2. Symptom-related genes found to be differentially expressed in livers from primary sclerosing cholangitis patients: Differentially expressed gene analysis results (logarithmic Fold Change, Average Expression and Adjusted p-values) are presented with respective machine learning predictive scores for supervised sample categories from the GSE61256 dataset (PSC versus other liver samples). Supplemental Table 3. Pavlidis Template Matching for FXR dependency in the liver transcriptome. Results of Pavlidis template analysis used to describe the FXR regulation dependency of PSC genes in liver samples from the GSE54557 dataset. For each gene, the R-Pearson correlation coefficient and its respective p-value are presented in this Table. Supplemental Table 4. Best one hundred genes found to be significant in the pseudotime trajectory of Abcb4-/- cholangiocytes. Best one hundred ranked genes found to be significant on the pseudotime cell trajectory of Abcb4-/- cholangiocytes based on the alternative expression of Nr0b2 and Sox9 in GSE168758.本研究论文配套的补充表格如下： 补充表1. 针对PubMed数据库中关联症状关键词的525个排名基因开展文本挖掘：本表格展示了通过「Génie」算法，结合3个医学主题词（Medical Subject Headings, MeSH）——胆道炎症、胆道纤维化与胆汁淤积进行文本挖掘所得到的525个排名基因，列示了每个基因对应各MeSH词的排名、p值以及PubMed文献编号（PMID）标识符。 补充表2. 原发性硬化性胆管炎（Primary Sclerosing Cholangitis, PSC）患者肝脏组织中差异表达的症状相关基因：本表格展示了差异表达基因分析结果，包括对数转换折叠变化（logarithmic Fold Change, logFC）、平均表达量与校正后p值，同时附带GSE61256数据集（PSC vs 其他肝脏样本）中监督样本分类的机器学习预测评分。 补充表3. 肝脏转录组中法尼醇X受体（Farnesoid X Receptor, FXR）依赖性的帕夫利迪斯模板匹配（Pavlidis Template Matching）分析：本表格展示了帕夫利迪斯模板匹配分析结果，用于描述GSE54557数据集肝脏样本中PSC相关基因的FXR调控依赖性，表格列示了每个基因的皮尔逊相关系数及其对应p值。 补充表4. Abcb4基因敲除（Abcb4-/-）胆管上皮细胞拟时间轨迹中筛选得到的前100个显著基因：本表格展示了基于GSE168758数据集中转录因子Nr0b2与Sox9的差异表达情况，在Abcb4-/-胆管上皮细胞的拟时间细胞轨迹中筛选出的排名前100的显著基因。