University of Illinois Urbana-Champaign

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

Blatti, Charles, III; 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

Permalink

https://hdl.handle.net/2142/106073

Description

Title
"Knowledge-guided analysis of ""omics"" data using the KnowEnG cloud platform"
Author(s)
  • Blatti, Charles, III
  • 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
Issue Date
2020-01-23
Keyword(s)
  • Genome analysis
  • Squamous cell carcinomas
  • Genetic networks
  • Somatic mutation
  • Gene expression
  • Cancer genomics
  • Computational pipelines
  • Transcriptome analysis
Abstract
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.
Publisher
Public Library of Science (PLoS)
Series/Report Name or Number
PLos Biology; vol. 18, no. 1, 2020
Type of Resource
text
Language
en
Permalink
http://hdl.handle.net/2142/106073
DOI
https://doi.org/10.1371/journal.pbio.3000583
Copyright and License Information
Copyright 2020 Charles Blatti III, Amin Emad, Matthew J. Berry, Lisa Gatzke, Milt Epstein, Daniel Lanier, Pramod Rizal, Jing Ge, Xiaoxia Liao, Omar Sobh, Mike Lambert, Corey S. Post, Jinfeng Xiao, Peter Groves, Aidan T. Epstein, Xi Chen, Subhashini Srinivasan, Erik Lehnert, Krishna R. Kalari, Liewei Wang, Richard M. Weinshilboum, Jun S. Song, C. Victor Jongeneel, Jiawei Han, Umberto Ravaioli, Nahil Sobh, Colleen B. Bushell, and Saurabh Sinha

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