Gene Set Analysis: Challenges, Opportunities, and Future Research

Frontiers in Genetics
Farhad MalekiAnthony J Kusalik

Abstract

Gene set analysis methods are widely used to provide insight into high-throughput gene expression data. There are many gene set analysis methods available. These methods rely on various assumptions and have different requirements, strengths and weaknesses. In this paper, we classify gene set analysis methods based on their components, describe the underlying requirements and assumptions for each class, and provide directions for future research in developing and evaluating gene set analysis methods.

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Citations

Dec 29, 2020·Development·Chad CockrumSusan Strome
Feb 24, 2021·Molecular Ecology·Oliver SelmoniVéronique Berteaux-Lecellier
Mar 25, 2021·Mathematical Biosciences and Engineering : MBE·Marios G KrokidisPanagiotis Vlamos
May 11, 2021·Statistics in Medicine·Shuoran Li, Lili Zhao
Jul 27, 2021·Development·Chad CockrumSusan Strome
Jul 25, 2021·International Journal of Molecular Sciences·Dario KringelJörn Lötsch
Aug 28, 2021·Biomolecules·Fotis A BaltoumasGeorgios A Pavlopoulos
Oct 5, 2021·Frontiers in Molecular Biosciences·Nico GerstnerHans-Peter Lenhof

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Methods Mentioned

BETA
RNA-Seq
FCS

Software Mentioned

Globaltest
TAPPA
TopologyGSA
PathNet
ORA
GSNCA
GSCA
SEA
SPIA
Clipper

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