Supporting information for BE1 experiment.

ccle.xlsx: Cancer Cell Line Encyclopedia (CCLE) derived information for 6 of the 7 cell lines used in BE1 experiment. The following files were retrieved from CCLE (ccle folder): Cell_lines_annotations_20181226.txt, CCLE_Fusions_20181130.txt, CCLE_metabolomics_20190502.csv, OmicsExpressionProteinCodingGenesTPMLogp1.csv, OmicsSomaticMutations.csv. Using the command.R script, in ccle folder, we extract only the information referring to the following cell lines: PC9, A549, NCI-H596,NCI-H1395, DV90, HCC78.Excel sheets:celllines: cell lines annotationfusions: detected fusion genesmetabolomic: dataset of 225 metabolite levels, profiled using liquid chromatography–mass spectrometry (LC-MS)log2TPM: gene expression, TPM values of the protein coding genes. Values are inferred from RNA-seq data using the RSEM tool and are reported after log2 transformation, using a pseudo-count of 1; log2(TPM+1)).somatic: all the somatic point mutations and indels called using Mutect2.drivers_genes_relations.xlsx: IPA/TRRUST2 derived Information referring to tumor driver genes (EGFR, MET, KRAS, BRAF, ERBB2, ALK, ROS1) expressed in the seven cell lines used in this experiment. The analysis was performed on IPA on June 2nd 2023 (this dataset folder ipa) and on TRRUST2 database (https://www.grnpedia.org/trrust/). For each driver gene (EGFR, MET, KRAS, BRAF, ERBB2, ALK, ROS1) were detected the directly connected genes (upstream and downstream) using grow function in IPA. The genes information and the connections were retrieved.Excel sheets:<b>all</b> type of connection detected<b>drivers-connections</b> all types of connection depicted in IPA for EGFR, MET, KRAS, BRAF, ERBB2, ALK, ROS1<b>activity</b> only functional connections, e.g. expression, activation. (IPA and TRRUST2)<b>activity 1st layer (v 2.0</b> only functional connections, e.g. expression, activation. (IPA and TRRUST2))<b>activity 2nd layer (v 2.0</b> only functional connections of the downstream genes from the 1st layer (e.g. 1st layer: ALK -&gt; MAPK3; 2nd layer MAPK3 -&gt; CDK4))<b>membership</b> expansion of the subset of IPA ids including multiple genes<b>modification</b> protein modification, e.g. phosphorylation<b>prot-prot</b> protein protein interaction<b>prot-DNA</b> protein-DNA interaction<b>XXX connected genes</b> description of the genes involved in the connections<br>

ccle.xlsx：包含源自癌症细胞系百科全书（Cancer Cell Line Encyclopedia，CCLE）的信息，对应BE1实验中使用的7种细胞系中的6种。以下文件均从CCLE的ccle文件夹中获取：Cell_lines_annotations_20181226.txt、CCLE_Fusions_20181130.txt、CCLE_metabolomics_20190502.csv、OmicsExpressionProteinCodingGenesTPMLogp1.csv、OmicsSomaticMutations.csv。通过ccle文件夹中的command.R脚本，我们仅提取了针对以下细胞系的相关信息：PC9、A549、NCI-H596、NCI-H1395、DV90、HCC78。该Excel文件包含以下工作表：
- celllines：细胞系注释信息
- fusions：已检测到的融合基因
- metabolomic：包含225种代谢物水平的数据集，采用液相色谱-质谱联用法（LC-MS）完成定量检测
- log2TPM：蛋白编码基因的基因表达量（TPM值）。该数据通过RSEM工具从RNA测序数据中推断得到，并以伪计数1进行log2转换后报告，格式为log2(TPM+1)
- somatic：所有通过Mutect2工具检测得到的体细胞点突变及插入缺失变异

drivers_genes_relations.xlsx：包含基于IPA/TRRUST2衍生的、针对本实验所用7种细胞系中表达的肿瘤驱动基因（EGFR、MET、KRAS、BRAF、ERBB2、ALK、ROS1）的相关信息。本次分析分别于2023年6月2日在IPA平台完成，以及基于TRRUST2数据库（https://www.grnpedia.org/trrust/）开展。针对每个驱动基因（EGFR、MET、KRAS、BRAF、ERBB2、ALK、ROS1），我们通过IPA中的grow函数检测了其直接上下游连接基因，并获取了相关基因信息及连接关系。
该Excel文件包含以下工作表：
- <b>all</b>：检测到的所有类型的连接关系
- drivers-connections：IPA平台中针对EGFR、MET、KRAS、BRAF、ERBB2、ALK、ROS1所展示的所有类型连接关系
- activity：仅包含功能连接关系，例如表达、激活（整合IPA与TRRUST2数据）
- activity 1st layer (v 2.0)：仅包含功能连接关系，例如表达、激活（整合IPA与TRRUST2数据）
- activity 2nd layer (v 2.0)：仅包含第一层连接基因的下游基因功能连接关系，例如第一层：ALK → MAPK3；第二层：MAPK3 → CDK4
- membership：包含多个基因的IPA标识符子集的扩展集合
- modification：蛋白质修饰关系，例如磷酸化
- prot-prot：蛋白质-蛋白质相互作用
- prot-DNA：蛋白质-DNA相互作用
- XXX connected genes：参与连接关系的基因相关说明