MSigDB swMATH ID: 40718 Software Authors: A. Liberzon Description: MSigDB: Molecular signatures database. The Molecular Signatures Database (MSigDB) is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis. Since its creation, MSigDB has grown beyond its roots in metabolic disease and cancer to include >10,000 gene sets. These better represent a wider range of biological processes and diseases, but the utility of the database is reduced by increased redundancy across, and heterogeneity within, gene sets. To address this challenge, here we use a combination of automated approaches and expert curation to develop a collection of “hallmark” gene sets as part of MSigDB. Each hallmark in this collection consists of a “refined” gene set, derived from multiple “founder” sets, that conveys a specific biological state or process and displays coherent expression. The hallmarks effectively summarize most of the relevant information of the original founder sets and, by reducing both variation and redundancy, provide more refined and concise inputs for gene set enrichment analysis. Homepage: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4707969/ Related Software: KEGG; STRING; GSVA; Bioconductor; Tensor2Tensor; COFACTOR; DeepGOPlus; DeepGO; QAUST; ProTranslator; GOLabeler; UDSMProt; DeepText2GO; NetGO; NewGOA; BLEU; GeneCards; InterProScan; BLAST; PSI-BLAST Cited in: 7 Publications all top 5 Cited by 33 Authors 1 Baladandayuthapani, Veerabhadran 1 Bharath, Karthik 1 Celeux, Gilles 1 Chute, John P. 1 Dameron, Olivier 1 Dressman, Holly 1 Gallopin, Mélina 1 Herazo-Maya, Jose D. 1 Hou, Mingliang 1 Jaffrézic, Florence 1 Kaminski, Naftali 1 Kong, Xiangjie 1 Kurtek, Sebastian 1 Lucas, Joseph Edward 1 Mohammed, Shariq 1 Nicolas, Jacques 1 Rao, Arvind U. K. 1 Rau, Andrea 1 Remy, Elisabeth 1 Ren, Jing 1 Siegel, Anne 1 Suchindran, Sunil 1 Sun, Jiehuan 1 Wang, Jane-Ling 1 Wang, Sheng 1 Wery, Méline 1 Xia, Feng 1 Xu, Hanwen 1 Yan, Xiao 1 Zhang, Da 1 Zhang, Dongyu 1 Zhao, Hongyu 1 Zheng, Lingling Cited in 4 Serials 3 Statistical Applications in Genetics and Molecular Biology 1 The Annals of Applied Statistics 1 Journal of Theoretical Biology 1 Computer Science Review Cited in 5 Fields 6 Biology and other natural sciences (92-XX) 3 Statistics (62-XX) 1 Combinatorics (05-XX) 1 Computer science (68-XX) 1 Information and communication theory, circuits (94-XX) Citations by Year