Gene set analysis: challenges, opportunities, and future research
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 …
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 …
evolution of healthcare practices and research. It has provided tools to accumulate, manage …
The reactome pathway knowledgebase
A Fabregat, S Jupe, L Matthews… - Nucleic acids …, 2018 - academic.oup.com
Abstract The Reactome Knowledgebase (https://reactome. org) provides molecular details of
signal transduction, transport, DNA replication, metabolism, and other cellular processes as …
signal transduction, transport, DNA replication, metabolism, and other cellular processes as …
Reactome pathway analysis: a high-performance in-memory approach
A Fabregat, K Sidiropoulos, G Viteri, O Forner… - BMC …, 2017 - Springer
Background Reactome aims to provide bioinformatics tools for visualisation, interpretation
and analysis of pathway knowledge to support basic research, genome analysis, modelling …
and analysis of pathway knowledge to support basic research, genome analysis, modelling …
Identifying significantly impacted pathways: a comprehensive review and assessment
Background Many high-throughput experiments compare two phenotypes such as disease
vs. healthy, with the goal of understanding the underlying biological phenomena …
vs. healthy, with the goal of understanding the underlying biological phenomena …
Enrichment map: a network-based method for gene-set enrichment visualization and interpretation
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 …
characterize large gene lists, such as the results of gene expression experiments. This …
Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis
C Wieder, C Frainay, N Poupin… - PLoS computational …, 2021 - journals.plos.org
Over-representation analysis (ORA) is one of the commonest pathway analysis approaches
used for the functional interpretation of metabolomics datasets. Despite the widespread use …
used for the functional interpretation of metabolomics datasets. Despite the widespread use …
Urgent need for consistent standards in functional enrichment analysis
K Wijesooriya, SA Jadaan, KL Perera… - PLoS computational …, 2022 - journals.plos.org
Gene set enrichment tests (aka functional enrichment analysis) are among the most
frequently used methods in computational biology. Despite this popularity, there are …
frequently used methods in computational biology. Despite this popularity, there are …
Ten years of pathway analysis: current approaches and outstanding challenges
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 …
of differentially expressed genes and proteins, as it reduces complexity and has increased …
PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
VK Mootha, CM Lindgren, KF Eriksson… - Nature …, 2003 - nature.com
DNA microarrays can be used to identify gene expression changes characteristic of human
disease. This is challenging, however, when relevant differences are subtle at the level of …
disease. This is challenging, however, when relevant differences are subtle at the level of …