Gene set analysis: challenges, opportunities, and future research

F Maleki, K Ovens, DJ Hogan, AJ Kusalik - Frontiers in genetics, 2020 - frontiersin.org
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 …

Big data analytics in healthcare

A Belle, R Thiagarajan… - BioMed research …, 2015 - Wiley Online Library
The rapidly expanding field of big data analytics has started to play a pivotal role in the
evolution of healthcare practices and research. It has provided tools to accumulate, manage …

Identifying significantly impacted pathways: a comprehensive review and assessment

TM Nguyen, A Shafi, T Nguyen, S Draghici - Genome biology, 2019 - Springer
Background Many high-throughput experiments compare two phenotypes such as disease
vs. healthy, with the goal of understanding the underlying biological phenomena …

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

DW Huang, BT Sherman, RA Lempicki - Nucleic acids research, 2009 - academic.oup.com
Functional analysis of large gene lists, derived in most cases from emerging high-throughput
genomic, proteomic and bioinformatics scanning approaches, is still a challenging and …

Enrichment map: a network-based method for gene-set enrichment visualization and interpretation

D Merico, R Isserlin, O Stueker, A Emili, GD Bader - PloS one, 2010 - journals.plos.org
Background Gene-set enrichment analysis is a useful technique to help functionally
characterize large gene lists, such as the results of gene expression experiments. This …

Ten years of pathway analysis: current approaches and outstanding challenges

P Khatri, M Sirota, AJ Butte - PLoS computational biology, 2012 - journals.plos.org
Pathway analysis has become the first choice for gaining insight into the underlying biology
of differentially expressed genes and proteins, as it reduces complexity and has increased …

MetPA: a web-based metabolomics tool for pathway analysis and visualization

J Xia, DS Wishart - Bioinformatics, 2010 - academic.oup.com
MetPA (Metabolomics Pathway Analysis) is a user-friendly, web-based tool dedicated to the
analysis and visualization of metabolomic data within the biological context of metabolic …

GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics

D Tabas-Madrid, R Nogales-Cadenas… - Nucleic acids …, 2012 - academic.oup.com
Since its first release in 2007, GeneCodis has become a valuable tool to functionally
interpret results from experimental techniques in genomics. This web-based application …

GO:: TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of …

EI Boyle, S Weng, J Gollub, H Jin, D Botstein… - …, 2004 - academic.oup.com
GO:: TermFinder comprises a set of object-oriented Perl modules for accessing Gene
Ontology (GO) information and evaluating and visualizing the collective annotation of a list of …

A novel signaling pathway impact analysis

AL Tarca, S Draghici, P Khatri, SS Hassan… - …, 2009 - academic.oup.com
Motivation: Gene expression class comparison studies may identify hundreds or thousands
of genes as differentially expressed (DE) between sample groups. Gaining biological insight …