DOI: 10.6084/m9.figshare.9973703.v2
title: Protein interaction networks and anatomy profiles used for "Integration of anatomy ontology data with protein-protein interaction networks" project

description: 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<br><b>The PPI networks retrieved from STRING and filtered by a gene similarity score cutoff</b><br>Mouse_string_filtered_PPI_network.txt: mouse PPI network filtered by 0.7 gene similarity score cutoff<br><br>Zebrafish_string_filtered_PPI_network: Zebrafish PPI network filtered by 0.7 gene similarity score cutoff<br><br><b>The pre-processed anatomy profiles used for construction and evaluation of the semantic networks</b><br>zebrafish_anatomy_profiles.txt<br><br>Mouse_anatomy_profiles.txt<br><b>Filtered anatomy-based gene networks for mouse</b><b><br></b>Filtered_lin_mouse_anatomy_network.txt: filtered by 0.9 gene similarity score cutoff<br>Filtered_resnik_mouse_anatomy_network.txt: filtered by 0.32 gene similarity score cutoff<br><br>Filtered_schlicker_mouse_anatomy_network.txt: filtered by 0.41 gene similarity score cutoff<br><br>Filtered_wang_mouse_anatomy_network.txt: filtered by 0.95 gene similarity score cutoff<br><br><b>Filtered anatomy-based gene networks for zebrafish</b><br>Filtered_lin_<b> </b>zebrafish_anatomy_network.txt: filtered by 0.55 gene similarity score cutoff<br>Filtered_resnik_zebrafish_anatomy_network.txt: filtered by 0.18 gene similarity score cutoff<br><br>Filtered_schlicker_zebrafish_anatomy_network.txt: filtered by 0.24 gene similarity score cutoff<br><br>Filtered_wang_zebrafish_anatomy_network.txt: filtered by 0.7 gene similarity score cutoff<br><b>Filtered integrated networks for mouse</b><br>Filtered_lin_mouse_integrated_network.txt: filtered by 0.9 gene similarity score cutoff<br>Filtered_resnik_mouse_integrated_network.txt: filtered by 0.32 gene similarity score cutoff<br><br>Filtered_schlicker_mouse_integrated_network.txt: filtered by 0.41 gene similarity score cutoff<br><br>Filtered_wang_mouse_integrated_network.txt: filtered by 0.95 gene similarity score cutoff<br><b>Filtered integrated networks for zebrafish</b><br>Filtered_lin_zebrafish_integrated_network.txt: filtered by 0.33 gene similarity score cutoff<br>Filtered_resnik_zebrafish_integrated_network.txt: filtered by 0.23 gene similarity score cutoff<br><br>Filtered_schlicker_zebrafish_integrated_network.txt: filtered by 0.24 gene similarity score cutoff<br><br>Filtered_wang_zebrafish_integrated_network.txt: filtered by 0.4 gene similarity score cutoff<b><br></b><b>Comparison with Random networks</b><b><br></b>Fully_random_zebrafish_wang_anatomy_network.txt: Fully randomized anatomy network equivalent to filtered zebrafish anatomy network for wang method<br><br>Fully_random_zebrafish_wang_integrated_network.txt: Fully randomized integrated network equivalent to filtered zebrafish integrated network for wang method<br><br>Random_profile_zebrafish_wang_anatomy_network.txt: The anatomy-based gene network generated by randomized profiles for zebrafish using wang method<br><br>Random_profile_zebrafish_wang_integrated_network.txt: The integrated network generated by randomized profiles for zebrafish using wang method<br><br>zebra_gene_randomizedprofiles.txt: The randomized profiles for zebrafish used to construct above networks<br><br><b>Construction of semantic networks and evaluation using randomly filtered 30 anatomy terms</b><br>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<br><br>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<br><br>zebra_30_removed_anatomy_profiles.txt: zebrafish anatomy profiles after randomly removing 30 anatomy terms. Used for network construction<br><br>zebrafish_30_uberon_term_profiles.txt: The zebrafish anatomy profiles generated using only the randomly removed 30 anatomy terms. Used for network evaluation.<br><b>Evaluation using GO-BP profiles</b><br>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<br><br><br>