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
Funding
Development of bioinformatics algorithms based on networks and Systems Biology for the search for new genes responsible for rare diseases of genetic origin
Instituto de Salud Carlos III
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