Protein interaction networks and anatomy profiles used for "Integration of anatomy ontology data with protein-protein interaction networks" project

Name: Protein interaction networks and anatomy profiles used for "Integration of anatomy ontology data with protein-protein interaction networks" project
Creator: figshare
Published: 2025-06-01 05:30:53
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DataCite Commons2025-06-01 更新2024-07-27 收录

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This repository contains the following protein interaction networks either retrieved from the STRING database or semantically constructed or integrated, and the anatomical profiles used for the construction and the evaluation of those networks The PPI networks retrieved from STRING and filtered by a gene similarity score cutoff Mouse_string_filtered_PPI_network.txt: mouse PPI network filtered by 0.7 gene similarity score cutoff Zebrafish_string_filtered_PPI_network: Zebrafish PPI network filtered by 0.7 gene similarity score cutoff The pre-processed anatomy profiles used for construction and evaluation of the semantic networks zebrafish_anatomy_profiles.txt Mouse_anatomy_profiles.txt Filtered anatomy-based gene networks for mouse Filtered_lin_mouse_anatomy_network.txt: filtered by 0.9 gene similarity score cutoff Filtered_resnik_mouse_anatomy_network.txt: filtered by 0.32 gene similarity score cutoff Filtered_schlicker_mouse_anatomy_network.txt: filtered by 0.41 gene similarity score cutoff Filtered_wang_mouse_anatomy_network.txt: filtered by 0.95 gene similarity score cutoff Filtered anatomy-based gene networks for zebrafish Filtered_lin_ zebrafish_anatomy_network.txt: filtered by 0.55 gene similarity score cutoff Filtered_resnik_zebrafish_anatomy_network.txt: filtered by 0.18 gene similarity score cutoff Filtered_schlicker_zebrafish_anatomy_network.txt: filtered by 0.24 gene similarity score cutoff Filtered_wang_zebrafish_anatomy_network.txt: filtered by 0.7 gene similarity score cutoff Filtered integrated networks for mouse Filtered_lin_mouse_integrated_network.txt: filtered by 0.9 gene similarity score cutoff Filtered_resnik_mouse_integrated_network.txt: filtered by 0.32 gene similarity score cutoff Filtered_schlicker_mouse_integrated_network.txt: filtered by 0.41 gene similarity score cutoff Filtered_wang_mouse_integrated_network.txt: filtered by 0.95 gene similarity score cutoff Filtered integrated networks for zebrafish Filtered_lin_zebrafish_integrated_network.txt: filtered by 0.33 gene similarity score cutoff Filtered_resnik_zebrafish_integrated_network.txt: filtered by 0.23 gene similarity score cutoff Filtered_schlicker_zebrafish_integrated_network.txt: filtered by 0.24 gene similarity score cutoff Filtered_wang_zebrafish_integrated_network.txt: filtered by 0.4 gene similarity score cutoff Comparison with Random networks Fully_random_zebrafish_wang_anatomy_network.txt: Fully randomized anatomy network equivalent to filtered zebrafish anatomy network for wang method Fully_random_zebrafish_wang_integrated_network.txt: Fully randomized integrated network equivalent to filtered zebrafish integrated network for wang method Random_profile_zebrafish_wang_anatomy_network.txt: The anatomy-based gene network generated by randomized profiles for zebrafish using wang method Random_profile_zebrafish_wang_integrated_network.txt: The integrated network generated by randomized profiles for zebrafish using wang method zebra_gene_randomizedprofiles.txt: The randomized profiles for zebrafish used to construct above networks Construction of semantic networks and evaluation using randomly filtered 30 anatomy terms Randomly_filtered_zebrafish_wang_anatomy_network.txt: The anatomy-based gene network generated using anatomy profiles after randomly removing 30 anatomy terms for zebrafish using wang method Randomly_filtered_zebrafish_wang_integrated_network.txt: The integrated network generated using anatomy profiles after randomly removing 30 anatomy terms for zebrafish using wang method zebra_30_removed_anatomy_profiles.txt: zebrafish anatomy profiles after randomly removing 30 anatomy terms. Used for network construction zebrafish_30_uberon_term_profiles.txt: The zebrafish anatomy profiles generated using only the randomly removed 30 anatomy terms. Used for network evaluation. Evaluation using GO-BP profiles zebra_goprofiles_modified.txt: the pre-processed zebrafish gene ontology- biological process term profiles used to evaluate the zebrafish wang integrated, anatomy-based and PPI networks

本仓库收录了以下数据：从STRING数据库检索得到、经语义构建或整合的蛋白质相互作用（Protein-Protein Interaction, PPI）网络，以及用于构建和评估上述网络的解剖学特征数据集 **从STRING数据库获取并经基因相似性得分阈值过滤的PPI网络** Mouse_string_filtered_PPI_network.txt：经0.7基因相似性得分阈值过滤的小鼠PPI网络文件 Zebrafish_string_filtered_PPI_network：经0.7基因相似性得分阈值过滤的斑马鱼PPI网络文件 **用于语义网络构建与评估的预处理解剖学特征集** zebrafish_anatomy_profiles.txt：斑马鱼解剖学特征文件 Mouse_anatomy_profiles.txt：小鼠解剖学特征文件 **小鼠过滤后的基于解剖学的基因网络** Filtered_lin_mouse_anatomy_network.txt：经0.9基因相似性得分阈值过滤的小鼠解剖学基因网络文件 Filtered_resnik_mouse_anatomy_network.txt：经0.32基因相似性得分阈值过滤的小鼠解剖学基因网络文件 Filtered_schlicker_mouse_anatomy_network.txt：经0.41基因相似性得分阈值过滤的小鼠解剖学基因网络文件 Filtered_wang_mouse_anatomy_network.txt：经0.95基因相似性得分阈值过滤的小鼠解剖学基因网络文件 **斑马鱼过滤后的基于解剖学的基因网络** Filtered_lin_zebrafish_anatomy_network.txt：经0.55基因相似性得分阈值过滤的斑马鱼解剖学基因网络文件 Filtered_resnik_zebrafish_anatomy_network.txt：经0.18基因相似性得分阈值过滤的斑马鱼解剖学基因网络文件 Filtered_schlicker_zebrafish_anatomy_network.txt：经0.24基因相似性得分阈值过滤的斑马鱼解剖学基因网络文件 Filtered_wang_zebrafish_anatomy_network.txt：经0.7基因相似性得分阈值过滤的斑马鱼解剖学基因网络文件 **小鼠过滤后的整合基因网络** Filtered_lin_mouse_integrated_network.txt：经0.9基因相似性得分阈值过滤的小鼠整合基因网络文件 Filtered_resnik_mouse_integrated_network.txt：经0.32基因相似性得分阈值过滤的小鼠整合基因网络文件 Filtered_schlicker_mouse_integrated_network.txt：经0.41基因相似性得分阈值过滤的小鼠整合基因网络文件 Filtered_wang_mouse_integrated_network.txt：经0.95基因相似性得分阈值过滤的小鼠整合基因网络文件 **斑马鱼过滤后的整合基因网络** Filtered_lin_zebrafish_integrated_network.txt：经0.33基因相似性得分阈值过滤的斑马鱼整合基因网络文件 Filtered_resnik_zebrafish_integrated_network.txt：经0.23基因相似性得分阈值过滤的斑马鱼整合基因网络文件 Filtered_schlicker_zebrafish_integrated_network.txt：经0.24基因相似性得分阈值过滤的斑马鱼整合基因网络文件 Filtered_wang_zebrafish_integrated_network.txt：经0.4基因相似性得分阈值过滤的斑马鱼整合基因网络文件 **与随机网络的对比数据集** Fully_random_zebrafish_wang_anatomy_network.txt：与采用wang方法过滤得到的斑马鱼解剖学网络等效的全随机斑马鱼解剖学网络文件 Fully_random_zebrafish_wang_integrated_network.txt：与采用wang方法过滤得到的斑马鱼整合网络等效的全随机斑马鱼整合网络文件 Random_profile_zebrafish_wang_anatomy_network.txt：采用wang方法、基于随机化基因特征集生成的斑马鱼解剖学基因网络文件 Random_profile_zebrafish_wang_integrated_network.txt：采用wang方法、基于随机化基因特征集生成的斑马鱼整合网络文件 zebra_gene_randomizedprofiles.txt：用于构建上述网络的斑马鱼随机化基因特征集文件 **使用随机筛选的30个解剖学术语构建语义网络并开展评估** Randomly_filtered_zebrafish_wang_anatomy_network.txt：采用wang方法、基于随机移除30个解剖学术语后的斑马鱼解剖学特征集生成的斑马鱼解剖学基因网络文件 Randomly_filtered_zebrafish_wang_integrated_network.txt：采用wang方法、基于随机移除30个解剖学术语后的斑马鱼解剖学特征集生成的斑马鱼整合网络文件 zebra_30_removed_anatomy_profiles.txt：经随机移除30个解剖学术语后的斑马鱼解剖学特征集，用于网络构建 zebrafish_30_uberon_term_profiles.txt：仅使用被随机移除的30个Uberon解剖学术语生成的斑马鱼解剖学特征集，用于网络评估 **使用基因本体-生物过程（Gene Ontology-Biological Process, GO-BP）特征集开展评估** zebra_goprofiles_modified.txt：经预处理的斑马鱼基因本体-生物过程术语特征集，用于评估斑马鱼采用wang方法得到的整合网络、解剖学基因网络及PPI网络

提供机构：

figshare

创建时间：

2019-10-12