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

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https://figshare.com/articles/dataset/Mouse_filtered_anatomy-based_gene_networks/9973703

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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

创建时间：

2019-10-12