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

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 networksThe PPI networks retrieved from STRING and filtered by a gene similarity score cutoffMouse_string_filtered_PPI_network.txt: mouse PPI network filtered by 0.7 gene similarity score cutoffZebrafish_string_filtered_PPI_network: Zebrafish PPI network filtered by 0.7 gene similarity score cutoffThe pre-processed anatomy profiles used for construction and evaluation of the semantic networkszebrafish_anatomy_profiles.txtMouse_anatomy_profiles.txtFiltered anatomy-based gene networks for mouseFiltered_lin_mouse_anatomy_network.txt: filtered by 0.9 gene similarity score cutoffFiltered_resnik_mouse_anatomy_network.txt: filtered by 0.32 gene similarity score cutoffFiltered_schlicker_mouse_anatomy_network.txt: filtered by 0.41 gene similarity score cutoffFiltered_wang_mouse_anatomy_network.txt: filtered by 0.95 gene similarity score cutoffFiltered anatomy-based gene networks for zebrafishFiltered_lin_ zebrafish_anatomy_network.txt: filtered by 0.55 gene similarity score cutoffFiltered_resnik_zebrafish_anatomy_network.txt: filtered by 0.18 gene similarity score cutoffFiltered_schlicker_zebrafish_anatomy_network.txt: filtered by 0.24 gene similarity score cutoffFiltered_wang_zebrafish_anatomy_network.txt: filtered by 0.7 gene similarity score cutoffFiltered integrated networks for mouseFiltered_lin_mouse_integrated_network.txt: filtered by 0.9 gene similarity score cutoffFiltered_resnik_mouse_integrated_network.txt: filtered by 0.32 gene similarity score cutoffFiltered_schlicker_mouse_integrated_network.txt: filtered by 0.41 gene similarity score cutoffFiltered_wang_mouse_integrated_network.txt: filtered by 0.95 gene similarity score cutoffFiltered integrated networks for zebrafishFiltered_lin_zebrafish_integrated_network.txt: filtered by 0.33 gene similarity score cutoffFiltered_resnik_zebrafish_integrated_network.txt: filtered by 0.23 gene similarity score cutoffFiltered_schlicker_zebrafish_integrated_network.txt: filtered by 0.24 gene similarity score cutoffFiltered_wang_zebrafish_integrated_network.txt: filtered by 0.4 gene similarity score cutoffComparison with Random networksFully_random_zebrafish_wang_anatomy_network.txt: Fully randomized anatomy network equivalent to filtered zebrafish anatomy network for wang methodFully_random_zebrafish_wang_integrated_network.txt: Fully randomized integrated network equivalent to filtered zebrafish integrated network for wang methodRandom_profile_zebrafish_wang_anatomy_network.txt: The anatomy-based gene network generated by randomized profiles for zebrafish using wang methodRandom_profile_zebrafish_wang_integrated_network.txt: The integrated network generated by randomized profiles for zebrafish using wang methodzebra_gene_randomizedprofiles.txt: The randomized profiles for zebrafish used to construct above networksConstruction of semantic networks and evaluation using randomly filtered 30 anatomy termsRandomly_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 methodRandomly_filtered_zebrafish_wang_integrated_network.txt: The integrated network generated using anatomy profiles after randomly removing 30 anatomy terms for zebrafish using wang methodzebra_30_removed_anatomy_profiles.txt: zebrafish anatomy profiles after randomly removing 30 anatomy terms. Used for network constructionzebrafish_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 profileszebra_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