Additional file 3 of Data- and expert-driven rule induction and filtering framework for functional interpretation and description of gene sets

Rule network sets that were generated as a result of this analysis. This excel file includes rule network sets that were generated as a result of this analysis. Each tab of the Excel file represents different rule set: set S01 represents results for the RuleGO method without filtering procedure applied, set S02 is a standard method with applied filtering, set S03 applies filtering using UTA approach, and set S04 proposes a new approach that allows the user to control the process of logical rule generation by providing a set of seed terms. For the set S04, we provide six rule sets obtained with different sets of quality assessment and filtering parameters as presented in Table 2. Each row represents a single rule, and GO terms from the expert set (seed terms) are denoted with star (*). Also for sets S02, S03, and S04 seed terms are marked with bold font. For each rule, we also provide the number of genes supported and recognized by the rule, its precision, coverage, value of the QCompound measure, p-value, and the list of genes supported by that rule. (XLSX 257 kb)

本分析生成的规则网络集。本Excel文件包含本次分析得到的规则网络集。该Excel文件的每个工作表对应一套不同的规则集：S01集对应未应用过滤流程的RuleGO方法结果；S02集为应用了过滤流程的标准方法结果；S03集采用UTA方法实施过滤；S04集则提出了一种新方法，允许用户通过提供种子术语（seed terms）集来调控逻辑规则的生成过程。针对S04集，我们提供了6组基于不同质量评估与过滤参数得到的规则集，具体参数详见表2。每一行代表一条独立规则，专家集（种子术语）内的基因本体（Gene Ontology, GO）术语将以星号（*）标注。此外，S02、S03及S04集中的种子术语均以粗体字体标识。对于每条规则，我们还提供了该规则所支持与识别的基因数量、精准率、覆盖度、QCompound测度值、p值，以及该规则所支持的基因列表。（XLSX格式，文件大小257 KB）