A side effect resource to capture phenotypic effects of drugs
TLDR
A public, computer‐readable side effect resource (SIDER) that connects 888 drugs to 1450 side effect terms and contains information on frequency in patients for one‐third of the drug–side effect pairs is developed.Abstract:
The molecular understanding of phenotypes caused by drugs in humans is essential for elucidating mechanisms of action and for developing personalized medicines. Side effects of drugs (also known as adverse drug reactions) are an important source of human phenotypic information, but so far research on this topic has been hampered by insufficient accessibility of data. Consequently, we have developed a public, computer-readable side effect resource (SIDER) that connects 888 drugs to 1450 side effect terms. It contains information on frequency in patients for one-third of the drug–side effect pairs. For 199 drugs, the side effect frequency of placebo administration could also be extracted. We illustrate the potential of SIDER with a number of analyses. The resource is freely available for academic research at http://sideeffects.embl.de.read more
Citations
More filters
Journal ArticleDOI
Network Medicine: A Network-Based Approach to Human Disease
TL;DR: Advances in this direction are essential for identifying new disease genes, for uncovering the biological significance of disease-associated mutations identified by genome-wide association studies and full-genome sequencing, and for identifying drug targets and biomarkers for complex diseases.
Journal ArticleDOI
The SIDER database of drugs and side effects
TL;DR: The SIDER (‘Side Effect Resource’, http://sideeffects.embl.de) database of drugs and ADRs contains a data set of drug indications, extracted from the package inserts using Natural Language Processing, used to reduce the rate of false positives by identifying medical terms that do not correspond to ADRs.
Journal ArticleDOI
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review
Peter Csermely,Tamas Korcsmaros,Tamas Korcsmaros,Huba Kiss,Gábor London,Ruth Nussinov,Ruth Nussinov +6 more
TL;DR: It is shown how network techniques can help in the identification of single-target, edgetic, multi-target and allo-network drug target candidates and an optimized protocol of network-aided drug development is suggested, and a list of systems-level hallmarks of drug quality is provided.
Journal ArticleDOI
Large-scale prediction and testing of drug activity on side-effect targets
Eugen Lounkine,Michael J. Keiser,Steven Whitebread,Dmitri Mikhailov,Jacques Hamon,Jeremy L. Jenkins,Paul Lavan,Eckhard Weber,Allison K. Doak,Serge Côté,Brian K. Shoichet,Laszlo Urban +11 more
TL;DR: An association metric is developed to prioritize those new off-targets that explained side effects better than any known target of a given drug, creating a drug–target–adverse drug reaction network and may have wide application to de-risking toxicological liabilities in drug discovery.
Journal ArticleDOI
PREDICT: a method for inferring novel drug indications with application to personalized medicine.
TL;DR: A novel method for the large‐scale prediction of drug indications (PREDICT) that can handle both approved drugs and novel molecules and lays the computational foundation for future personalized drug treatments, where gene expression signatures from individual patients would replace the disease‐specific signatures.
References
More filters
Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI
Drug repositioning: identifying and developing new uses for existing drugs
Ted T. Ashburn,Karl B. Thor +1 more
TL;DR: Repositioning existing drugs for new indications could deliver the productivity increases that the industry needs while shifting the locus of production to biotechnology companies.
Journal ArticleDOI
DrugBank: a knowledgebase for drugs, drug actions and drug targets
David S. Wishart,Craig Knox,An Chi Guo,Dean Cheng,Savita Shrivastava,Dan Tzur,Bijaya Gautam,Murtaza Hassanali +7 more
TL;DR: The latest version of DrugBank (release 2.0) has been expanded significantly over the previous release and contains 60% more FDA-approved small molecule and biotech drugs including 10% more ‘experimental’ drugs.
Journal ArticleDOI
BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities
TL;DR: BindingDB is a publicly accessible database currently containing ∼20 000 experimentally determined binding affinities of protein–ligand complexes, for 110 protein targets including isoforms and mutational variants, and ∼11000 small molecule ligands.
Journal ArticleDOI
Drug Target Identification Using Side-Effect Similarity
Monica Campillos,Michael Kuhn,Anne-Claude Gavin,Lars Juhl Jensen,Lars Juhl Jensen,Peer Bork,Peer Bork +6 more
TL;DR: Applied to 746 marketed drugs, a network of 1018 side effect–driven drug-drug relations became apparent, 261 of which are formed by chemically dissimilar drugs from different therapeutic indications, hinting at new uses of marketed drugs.
Related Papers (5)
The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease
Justin Lamb,Emily D. Crawford,David Peck,Joshua W. Modell,Irene C. Blat,Matthew J. Wrobel,Jim Lerner,Jean Philippe Brunet,Aravind Subramanian,Kenneth N. Ross,Michael Reich,Haley Hieronymus,Haley Hieronymus,Guo Wei,Guo Wei,Scott A. Armstrong,Scott A. Armstrong,Stephen J. Haggarty,Stephen J. Haggarty,Paul A. Clemons,Ru Wei,Steven A. Carr,Eric S. Lander,Eric S. Lander,Todd R. Golub +24 more