Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform

• Published in: PLoS biology 2020-01, Vol.18 (1), p.e3000583-e3000583
• Main Authors: Blatti, 3rd, Charles, Emad, Amin, Berry, Matthew J, Gatzke, Lisa, Epstein, Milt, Lanier, Daniel, Rizal, Pramod, Ge, Jing, Liao, Xiaoxia, Sobh, Omar, Lambert, Mike, Post, Corey S, Xiao, Jinfeng, Groves, Peter, Epstein, Aidan T, Chen, Xi, Srinivasan, Subhashini, Lehnert, Erik, Kalari, Krishna R, Wang, Liewei, Weinshilboum, Richard M, Song, Jun S, Jongeneel, C Victor, Han, Jiawei, Ravaioli, Umberto, Sobh, Nahil, Bushell, Colleen B, Sinha, Saurabh
• Format: Article
• Language: English
• Subjects: Algorithms; Bioinformatics; Biology; Biology and Life Sciences; Cancer; Case studies; Cloud Computing; Cluster Analysis; Clustering; Computational Biology - methods; Computer and Information Sciences; Computer applications; Computer engineering; Computer science; Cost analysis; Data Analysis; Data mining; Data Mining - methods; Datasets; Datasets as Topic; Gene expression; Genomes; Genomics; Genomics - methods; High-Throughput Nucleotide Sequencing - methods; Humans; Knowledge; Knowledge bases (artificial intelligence); Learning algorithms; Logos; Machine Learning; Medicine and Health Sciences; Metabolomics - methods; Methods and Resources; Research and Analysis Methods; Signature analysis; Software; Squamous cell carcinoma; Supervision; Web portals
• ISSN: 1545-7885; 1544-9173; 1545-7885
• DOI: 10.1371/journal.pbio.3000583

We present Knowledge Engine for Genomics (KnowEnG), a free-to-use computational system for analysis of genomics data sets, designed to accelerate biomedical discovery. It includes tools for popular bioinformatics tasks such as gene prioritization, sample clustering, gene set analysis, and expression signature analysis. The system specializes in "knowledge-guided" data mining and machine learning algorithms, in which user-provided data are analyzed in light of prior information about genes, aggregated from numerous knowledge bases and encoded in a massive "Knowledge Network." KnowEnG adheres to "FAIR" principles (findable, accessible, interoperable, and reuseable): its tools are easily portable to diverse computing environments, run on the cloud for scalable and cost-effective execution, and are interoperable with other computing platforms. The analysis tools are made available through multiple access modes, including a web portal with specialized visualization modules. We demonstrate the KnowEnG system's potential value in democratization of advanced tools for the modern genomics era through several case studies that use its tools to recreate and expand upon the published analysis of cancer data sets.