GLOWgenesNets.zip

<p>Set of networks of gene-gene functional associations to be used as input of GLOWgenes, a network-based algorithm to predict new gene-phenotype associations tunned to be applied in the discovery of new candidate genes in rare genetic diseases. GLOWgenes is available at www.glowgenes.org. It is developed by the https://www.translationalbioinformaticslab.es.</p> <p><br></p> <p><em><strong>SOURCES</strong></em></p> <p>         </p> <p><strong>Network, Knowledge Category, Edges weights, Data source, reference</strong></p> <p>Textmining-STRING, COCITATION, Textmining score, STRING v11, <a href="https://string-db.org/cgi/download.pl" target="_blank"><u>https://string-db.org/cgi/download.pl</u></a>, Szklarczyk et al,. 2019</p> <p>COXPRESdb, COEXPRESSION, Inverse of the Mutual Rank value, COXPRESdb v7 - Hsa-u.c2-0, <a href="https://coxpresdb.jp/download/Hsa-u.c2-0/coex/" target="_blank"><u>https://coxpresdb.jp/download/Hsa-u.c2-0/</u></a>, Obayashi et al., 2019</p> <p>Coexpression-STRING, COEXPRESSION, Coexpression channel score, STRING v11, <a href="https://string-db.org/cgi/download.pl" target="_blank"><u>https://string-db.org/cgi/download.pl</u></a>, Szklarczyk et al., 2019</p> <p>Coregulation map, COEXPRESSION, NA, ProteomeHD - top-scoring 0.5%, <a href="https://www.proteomehd.net/download" target="_blank"><u>https://www.proteomehd.net/</u></a><a href="https://www.proteomehd.net/download" target="_blank"><u>download</u></a>, Kustatscher et al.,2019</p> <p>Experimental subcellular map, COLOCALIZATION, NA, Subcellular Localization Experimental Map, <a href="http://science.sciencemag.org/highwire/filestream/694217/field_highwire_adjunct_files/9/aal3321_Thul_SM_table_S17.xlsx" target="_blank"><u>http://</u></a><a href="http://science.sciencemag.org/highwire/filestream/694217/field_highwire_adjunct_files/9/aal3321_Thul_SM_table_S17.xlsx" target="_blank"><u>science.sciencemag.org/highwire/filestream/694217/field_highwire_adjunct_files/9/aal3321_Thul_SM_table_S17.xlsx</u></a>, Thul et al., 2017</p> <p>Cellular Component similarity - GO, COLOCALIZATION, Semantic similarity scores, Gene Ontology CC ontology, <a href="http://geneontology.org/docs/download-ontology/" target="_blank"><u>http://geneontology.org/docs/download-ontology/</u></a>, The Gene Ontology Consortium, 2019; Zhao et a.l. 2018</p> <p>Experimental - STRING, PPI, NA, STRING v11 - experimental channel, <a href="https://string-db.org/cgi/download.pl" target="_blank"><u>https://string-db.org/cgi/download.pl</u></a>, Szklarczyk et al.,. 2019</p> <p>Physical PPI - BIOGRID, PPI, NA, BIOGRID 4.2, <a href="https://downloads.thebiogrid.org/BioGRID" target="_blank"><u>https://downloads.thebiogrid.org/BioGRID</u></a>, Oughtred et al., 2019</p> <p>HuRI physical PPI, PPI, NA, The Human Reference Interactome, <a href="http://www.interactome-atlas.org/" target="_blank"><u>http://www.interactome-atlas.org/</u></a>, Luck et al., 2020</p> <p>HI-union physical PPI, PPI, NA, The Human Reference Interactome, <a href="http://www.interactome-atlas.org/" target="_blank"><u>http://www.interactome-atlas.org/</u></a>, Luck et al,. 2020</p> <p>Reactome pathways, PATHWAYS, NA, Reactome, <a href="https://reactome.org/download-data" target="_blank"><u>https://reactome.org/download-data</u></a>, Jassal et al,. 2020</p> <p>Reactome FI, PATHWAYS, NA, Pathway-based functional interaction network - v2018, <a href="https://reactome.org/about/news/133-reactomefiviz-app-version-7-2-0-released" target="_blank"><u>https://reactome.org/about/news/133-reactomefiviz-app-version-7-2-0-released</u></a>, Wu y Haw  et al,. 2017</p> <p>Database - STRING, PATHWAYS, NA, STRING v11 - database channel, <a href="https://string-db.org/cgi/download.pl" target="_blank"><u>https://string-db.org/cgi/download.pl</u></a>, Szklarczyk et al,. 2019</p> <p>Molecular function similarity, FUNCTIONAL ANNOTATION, Semantic similarity scores, Gene Ontology MF ontology, <a href="http://geneontology.org/docs/download-ontology/" target="_blank"><u>http://geneontology.org/docs/download-ontology/</u></a>, The Gene Ontology Consortium, 2019; Zhao et a.l. 2018.</p> <p>Biological process similarity, FUNCTIONAL ANNOTATION, Semantic similarity scores, Gene Ontology BP ontology, <a href="http://geneontology.org/docs/download-ontology/" target="_blank"><u>http://geneontology.org/docs/download-ontology/</u></a>, The Gene Ontology Consortium, 2019; Zhao et a.l. 2018.</p> <p>hu.MAP co-complex, COMPLEXES, NA, hu.MAP Experimental Map, <a href="http://hu.proteincomplexes.org/download" target="_blank"><u>http://hu.proteincomplexes.org/</u></a><a href="http://hu.proteincomplexes.org/download" target="_blank"><u>download</u></a>, Drew et al. 2017  </p> <p>CORUM co-complex, COMPLEXES, NA, CORUM, <a href="http://mips.helmholtz-muenchen.de/corum/download/coreComplexes.txt.zip" target="_blank"><u>http://mips.helmholtz-muenchen.de/corum/download/coreComplexes.txt.zip</u></a>, Giurgiu et al., 2019</p> <p>Genetic - Rauscher et al., COESSENTIALITY, NA, Genetic Interaction Network from 85 CRISPR/Cas9 screens in human cancer cells, <a href="https://www.embopress.org/doi/full/10.15252/msb.20177656" target="_blank"><u>https://www.embopress.org/doi/full/10.15252/msb.20177656</u></a>, Rauscher et al. 2018</p> <p>Coessentiality - Kim et al., COESSENTIALITY, weighted co-essentiality, 276 high-quality CRISPR knockout screens in cancer cell lines, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6464042/bin/LSA-2018-00278_TableS5.txt" target="_blank"><u>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6464042/bin/LSA-2018-00278_TableS5.txt</u></a>, Kim et al. 2019</p> <p>Fitness RNAi, COESSENTIALITY, gene fitness rank correlation coefficients, <em>501 cancer cell lines – RNAi - Achilles Project, </em>Reproduced following Pan et al. 2018 <a href="https://figshare.com/articles/dataset/Pan_Meyers_et_al_Cell_Systems_2018_/6005297" target="_blank"><u>https://figshare.com/articles/dataset/Pan_Meyers_et_al_Cell_Systems_2018_/6005297</u></a><em>, Pan et al., 2018</em></p> <p>Fitness <em>CRISPR, </em>COESSENTIALITY, NA, <em>342 cancer cell lines – CRISPR-Cas - Achilles Project, </em>Reproduced following  Pan et al. 2018 <a href="https://figshare.com/articles/dataset/Pan_Meyers_et_al_Cell_Systems_2018_/6005297" target="_blank"><u>https://figshare.com/articles/dataset/Pan_Meyers_et_al_Cell_Systems_2</u></a><a href="https://figshare.com/articles/dataset/Pan_Meyers_et_al_Cell_Systems_2018_/6005297" target="_blank"><u>018_/6005297</u></a><em>, Pan et al., 2018</em></p> <p>Genetic - BIOGRID, COESSENTIALITY, NA, BIOGRID 4.2, <a href="https://downloads.thebiogrid.org/BioGRID" target="_blank"><u>https://downloads.thebiogrid.org/BioGRID</u></a>, Oughtred et al., 2019</p> <p>DoRothEA regulation, REGULATION, evidence levels  transformed into numeric values and normalized to 0-1 range, DOROTHEA, saezlab.github.io/DoRothEA, García-Alonso et al.,  2019</p> <p>TRANSFAC regulation, REGULATION, NA, TRANSFAC, NDEX, Wingender et al., 2008</p> <p>TTRUST regulation, REGULATION, NA, TTRUSTv2, <a href="https://www.grnpedia.org/trrust/" target="_blank"><u>https://www.grnpedia.org/trrust/</u></a>, Han et al., 2018</p> <p>RegNetwork, REGULATION, NA, RegNetwork, <a href="http://www.regnetworkweb.org/" target="_blank"><u>http://www.regnetworkweb.org/</u></a>, Liu et al., 2015</p> <p>HPO similarity, PHENOTYPE, Z-scores in the distribution of Jaccard values, HPO similarity, <a href="https://hpo.jax.org/app/download/annotation" target="_blank"><u>https://hpo.jax.org/app/download/annotation</u></a>, Köhler et al,. 2017</p> <p>Extended HPO similarity, PHENOTYPE, Z-scores in the distribution of Jaccard values, HPO similarity, <a href="https://hpo.jax.org/app/download/annotation" target="_blank"><u>https://hpo.jax.org/app/download/annotation</u></a>, Köhler et al,. 2017</p> <p>Phenotype -  MGI, MOUSE MODELS, Z-scores in the distribution of Jaccard values, MGIphenotype similarity, <a href="http://www.informatics.jax.org/downloads/reports/index.html" target="_blank"><u>http://www.informatics.jax.org/downloads/reports/index.html</u></a>, Bult et al., 2019</p> <p>DGIdb similarity, DRUG SHARING, NA, DGIdb Drug-Gene interactions, <a href="http://www.dgidb.org/downloads" target="_blank"><u>http://www.dgidb.org/</u></a><a href="http://www.dgidb.org/downloads" target="_blank"><u>downloads, </u></a>Cotto et al,. 2019</p> <p>Neighborhood - STRING, GENOMIC LOCALIZATION, NA, STRING v11-  neighborhood channel, <a href="https://string-db.org/cgi/download.pl" target="_blank"><u>https://string-db.org/cgi/</u></a><a href="https://string-db.org/cgi/download.pl" target="_blank"><u>download.pl</u></a>, Szklarczyk et al. 2019</p> <p>Coocurrence - STRING, GENOMIC LOCALIZATION, NA, STRING v11-  coocurrence channel, <a href="https://string-db.org/cgi/download.pl" target="_blank"><u>https://string-db.org/cgi/download.pl</u></a>, Szklarczyk et al. 2019</p> <p>Fusion - STRING, GENOMIC LOCALIZATION, NA, STRING v11-  fusion channel, <a href="https://string-db.org/cgi/download.pl" target="_blank"><u>https://string-db.org/cgi/download.pl</u></a>, Szklarczyk et al. 2019</p>