Data for "Peroxisomal interactome mapping enables network-based modelling of function and disease." by Gersting et al.

This data includes all necessary files to reproduce the results of the paper "Peroxisomal interactome mapping enables network-based modelling of function and disease." by Gersting et al. To reproduce the findings of this publication, Python and R code are made available via github. All files provided here must be downloaded in order to execute the provided code. The files NCBI_Homo_sapiens.gene_info, GO_gene2go and HGNC_gene_with_protein_product.txt contain the publicly available data from https://ftp.ncbi.nih.gov and https://www.genenames.org/download/. However these databases do not offer archived data. To provide reproducibility the files downloaded the 26th August 2023 are made available here. The file filtered_merged_HuRI_MINT_IntAct_BioGrid.csv contains the integrated data of the protein protein interaction databases HuRI, MINT, IntAct and Biogrid (downloaded the 26th August 2026) for more details see methods section of the provided publication. The files Bret_screen_entrez_final.txt and PEX_genes_final.xlsx contain the protein protein interaction data identified via iBRET and list of peroxisomal proteins investigated. proteins_lysosome_expert_curated.xlsx contains a expert curated list of lysosomal proteins. The Yifrach_adapted.xlsx contains the set of peroxisomal proteins as published by Yifrach et al. (DOI: 10.1007/978-981-13-2233-4_2). An overview of the reference data set can be found in PRS_overview.txt for the "positive" reference data set and RRS_overview.txt for the "random / negativ" reference data set RawData of measurement of the reference data sets can be found in reference_data_pex_interactome.txt and reference_data_pex11_interactome.txt Description of data format for interactions measurements:Column 1 and 2 identifier of experimentColumn 3: protein 1Column 4: Description of the tag for protein 1 in format T-P, where T may be C or N and P hRluc or VenusColumn 5: protein 2Column 6: Description of the tag for protein 2, same format as for Column 4Column 7: identifier of experimentColumn 8: Donor to acceptor ratio, format donor:acceptorColumn 9: Type; either PRS (positive reference data set) or RRS (random reference data set) The following columns provide actual data values:First we have 2 columns for all hRluc values, then 2 columns for all Venus values and finally 2 columns for BRET-ratios (pre-calculated). The last column may contain the average BRET ratio.本数据集包含复现Gersting等人发表的论文《过氧化物酶体相互作用组图谱构建助力功能与疾病的网络建模》（原标题："Peroxisomal interactome mapping enables network-based modelling of function and disease"）所需的全部必要文件。 为复现本研究的实验结果，我们通过GitHub开源了配套的Python与R代码。运行此代码需下载本文档提供的全部文件。 文件NCBI_Homo_sapiens.gene_info、GO_gene2go及HGNC_gene_with_protein_product.txt包含取自https://ftp.ncbi.nih.gov与https://www.genenames.org/download/的公开可用数据。但上述数据库未提供存档版本，为确保实验可复现，我们在此提供2023年8月26日下载的对应文件。 文件filtered_merged_HuRI_MINT_IntAct_BioGrid.csv包含整合后的蛋白质相互作用数据库HuRI、MINT、IntAct与BioGRID的整合数据（下载于2026年8月26日），详细信息请参阅配套论文的方法部分。 文件Bret_screen_entrez_final.txt与PEX_genes_final.xlsx分别包含通过iBRET技术鉴定得到的蛋白质相互作用数据，以及本次研究涉及的过氧化物酶体蛋白列表。 文件proteins_lysosome_expert_curated.xlsx包含经专家人工注释的溶酶体蛋白列表。 文件Yifrach_adapted.xlsx包含Yifrach等人发表的过氧化物酶体蛋白集（DOI: 10.1007/978-981-13-2233-4_2）。 参考数据集的概况可分别从PRS_overview.txt（对应“阳性参考数据集”）与RRS_overview.txt（对应“随机/阴性参考数据集”）中查阅。 参考数据集的实验测量原始数据可于reference_data_pex_interactome.txt与reference_data_pex11_interactome.txt中获取。 相互作用测量的数据格式说明如下： 1. 第1、2列：实验标识符 2. 第3列：蛋白1 3. 第4列：蛋白1的标签描述，格式为T-P，其中T可取C或N，P可取hRluc或Venus 4. 第5列：蛋白2 5. 第6列：蛋白2的标签描述，格式与第4列一致 6. 第7列：实验标识符 7. 第8列：供体-受体比值，格式为供体:受体 8. 第9列：数据集类型，仅可为PRS（阳性参考数据集）或RRS（随机参考数据集） 后续列包含实际测量数据：首先是2列hRluc信号值，其次是2列Venus信号值，最后是2列预先计算得到的BRET比值。 最后一列可为平均BRET比值。