Article

Benchmarking enrichment analysis methods with the disease pathway network

2023-09-30

Abstract excerpt

<h4>ABSTRACT</h4> Enrichment analysis (EA) is a common approach to gain functional insights from genome-scale experiments. As a consequence, a large number of EA methods have been developed, yet it is unclear from previous studies which method is the best for a given dataset. The main issues with previous benchmarks include the complexity of correctly assigning true pathways to a test dataset, and lack of general...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 909b1bdd-7f47-55c0-b733-85fd5305eda0
DOI: 10.1101/2023.09.29.560169

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Benchmarking enrichment analysis methods with the disease pathway networkDOI 10.1101/2023.09.29.560169Read

Towards a gold standard for benchmarking gene set enrichment analysisSemantic proximity Read

Gene set correlation enrichment analysis for interpreting and annotating gene expression profiles.Semantic proximity Read

Using Published Pathway Figures in Enrichment Analysis and Machine LearningSemantic proximity Read

SLEPR: a sample-level enrichment-based pathway ranking method -- seeking biological themes through pathway-level consistency.Semantic proximity Read

CTpathway: a CrossTalk-based pathway enrichment analysis method for cancer researchSemantic proximity Read

NGSEA: network-based gene set enrichment analysis for interpreting gene expression phenotypes with functional gene setsSemantic proximity Read

Gene set enrichment; a problem of pathways.Semantic proximity Read

Differential Expression Enrichment Tool (DEET): An interactive atlas of human differential gene expressionSemantic proximity Read

Pathway-based biomarker identification with crosstalk analysis for robust prognosis prediction in hepatocellular carcinomaSemantic proximity Read

The Pathway Coexpression Network: Revealing pathway relationshipsSemantic proximity Read

Robust and clinically relevant prediction of response to anti-cancer drugs via network integration of molecular profilesSemantic proximity Read

Combining multiple tools outperforms individual methods in gene set enrichment analysesSemantic proximity Read