GLOWgenesNets.zip

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.

SOURCES

         

Network, Knowledge Category, Edges weights, Data source, reference

Textmining-STRING, COCITATION, Textmining score, STRING v11, https://string-db.org/cgi/download.pl, Szklarczyk et al,. 2019

COXPRESdb, COEXPRESSION, Inverse of the Mutual Rank value, COXPRESdb v7 - Hsa-u.c2-0, https://coxpresdb.jp/download/Hsa-u.c2-0/, Obayashi et al., 2019

Coexpression-STRING, COEXPRESSION, Coexpression channel score, STRING v11, https://string-db.org/cgi/download.pl, Szklarczyk et al., 2019

Coregulation map, COEXPRESSION, NA, ProteomeHD - top-scoring 0.5%, https://www.proteomehd.net/download, Kustatscher et al.,2019

Experimental subcellular map, COLOCALIZATION, NA, Subcellular Localization Experimental Map, http://science.sciencemag.org/highwire/filestream/694217/field_highwire_adjunct_files/9/aal3321_Thul_SM_table_S17.xlsx, Thul et al., 2017

Cellular Component similarity - GO, COLOCALIZATION, Semantic similarity scores, Gene Ontology CC ontology, http://geneontology.org/docs/download-ontology/, The Gene Ontology Consortium, 2019; Zhao et a.l. 2018

Experimental - STRING, PPI, NA, STRING v11 - experimental channel, https://string-db.org/cgi/download.pl, Szklarczyk et al.,. 2019

Physical PPI - BIOGRID, PPI, NA, BIOGRID 4.2, https://downloads.thebiogrid.org/BioGRID, Oughtred et al., 2019

HuRI physical PPI, PPI, NA, The Human Reference Interactome, http://www.interactome-atlas.org/, Luck et al., 2020

HI-union physical PPI, PPI, NA, The Human Reference Interactome, http://www.interactome-atlas.org/, Luck et al,. 2020

Reactome pathways, PATHWAYS, NA, Reactome, https://reactome.org/download-data, Jassal et al,. 2020

Reactome FI, PATHWAYS, NA, Pathway-based functional interaction network - v2018, https://reactome.org/about/news/133-reactomefiviz-app-version-7-2-0-released, Wu y Haw  et al,. 2017

Database - STRING, PATHWAYS, NA, STRING v11 - database channel, https://string-db.org/cgi/download.pl, Szklarczyk et al,. 2019

Molecular function similarity, FUNCTIONAL ANNOTATION, Semantic similarity scores, Gene Ontology MF ontology, http://geneontology.org/docs/download-ontology/, The Gene Ontology Consortium, 2019; Zhao et a.l. 2018.

Biological process similarity, FUNCTIONAL ANNOTATION, Semantic similarity scores, Gene Ontology BP ontology, http://geneontology.org/docs/download-ontology/, The Gene Ontology Consortium, 2019; Zhao et a.l. 2018.

hu.MAP co-complex, COMPLEXES, NA, hu.MAP Experimental Map, http://hu.proteincomplexes.org/download, Drew et al. 2017  

CORUM co-complex, COMPLEXES, NA, CORUM, http://mips.helmholtz-muenchen.de/corum/download/coreComplexes.txt.zip, Giurgiu et al., 2019

Genetic - Rauscher et al., COESSENTIALITY, NA, Genetic Interaction Network from 85 CRISPR/Cas9 screens in human cancer cells, https://www.embopress.org/doi/full/10.15252/msb.20177656, Rauscher et al. 2018

Coessentiality - Kim et al., COESSENTIALITY, weighted co-essentiality, 276 high-quality CRISPR knockout screens in cancer cell lines, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6464042/bin/LSA-2018-00278_TableS5.txt, Kim et al. 2019

Fitness RNAi, COESSENTIALITY, gene fitness rank correlation coefficients, 501 cancer cell lines – RNAi - Achilles Project, Reproduced following Pan et al. 2018 https://figshare.com/articles/dataset/Pan_Meyers_et_al_Cell_Systems_2018_/6005297, Pan et al., 2018

Fitness CRISPR, COESSENTIALITY, NA, 342 cancer cell lines – CRISPR-Cas - Achilles Project, Reproduced following  Pan et al. 2018 https://figshare.com/articles/dataset/Pan_Meyers_et_al_Cell_Systems_2018_/6005297, Pan et al., 2018

Genetic - BIOGRID, COESSENTIALITY, NA, BIOGRID 4.2, https://downloads.thebiogrid.org/BioGRID, Oughtred et al., 2019

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

TRANSFAC regulation, REGULATION, NA, TRANSFAC, NDEX, Wingender et al., 2008

TTRUST regulation, REGULATION, NA, TTRUSTv2, https://www.grnpedia.org/trrust/, Han et al., 2018

RegNetwork, REGULATION, NA, RegNetwork, http://www.regnetworkweb.org/, Liu et al., 2015

HPO similarity, PHENOTYPE, Z-scores in the distribution of Jaccard values, HPO similarity, https://hpo.jax.org/app/download/annotation, Köhler et al,. 2017

Extended HPO similarity, PHENOTYPE, Z-scores in the distribution of Jaccard values, HPO similarity, https://hpo.jax.org/app/download/annotation, Köhler et al,. 2017

Phenotype -  MGI, MOUSE MODELS, Z-scores in the distribution of Jaccard values, MGIphenotype similarity, http://www.informatics.jax.org/downloads/reports/index.html, Bult et al., 2019

DGIdb similarity, DRUG SHARING, NA, DGIdb Drug-Gene interactions, http://www.dgidb.org/downloads, Cotto et al,. 2019

Neighborhood - STRING, GENOMIC LOCALIZATION, NA, STRING v11-  neighborhood channel, https://string-db.org/cgi/download.pl, Szklarczyk et al. 2019

Coocurrence - STRING, GENOMIC LOCALIZATION, NA, STRING v11-  coocurrence channel, https://string-db.org/cgi/download.pl, Szklarczyk et al. 2019

Fusion - STRING, GENOMIC LOCALIZATION, NA, STRING v11-  fusion channel, https://string-db.org/cgi/download.pl, Szklarczyk et al. 2019