ArticleBioinformatics (Oxford, England)2017
FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
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- scFPC-DE: Robust Differential Expression Analysis Along Single Cell Trajectories via Functional Principal Component Analysis.bioRxiv : the preprint server for biology · 2025Article
- Alzheimer's disease: an integrative bioinformatics and machine learning analysis reveals glutamine metabolism-associated gene biomarkers.BMC pharmacology & toxicology · 2025Article
- Purine metabolism-related genes and immunization in thyroid eye disease were validated using bioinformatics and machine learning.Scientific reports · 2023Article
- SMYD3 associates with the NuRD (MTA1/2) complex to regulate transcription and promote proliferation and invasiveness in hepatocellular carcinoma cells.BMC biology · 2022Article
- FastMix: a versatile data integration pipeline for cell type-specific biomarker inference.Bioinformatics (Oxford, England) · 2022Article
- QPRT Acts as an Independent Prognostic Factor in Invasive Breast Cancer.Journal of oncology · 2022Article
- Expression and clinical significance ofInternational journal of clinical and experimental pathology · 2021Article
- A Novel Six-Gene Signature for Prognosis Prediction in Ovarian Cancer.Frontiers in genetics · 2020Article
- Bioinformatics identification of potential genes and pathways in preeclampsia based on functional gene set enrichment analyses.Experimental and therapeutic medicine · 2019Article
- High expression ofWorld journal of gastroenterology · 2019Article
- Aims, Study Design, and Enrollment Results From the Assessing Predictors of Infant Respiratory Syncytial Virus Effects and Severity Study.JMIR research protocols · 2019Article
- Highly efficient hypothesis testing methods for regression-type tests with correlated observations and heterogeneous variance structure.BMC bioinformatics · 2019Article
- Epigenetic Profiles Reveal That ADCYAP1 Serves as Key Molecule in Gestational Diabetes Mellitus.Computational and mathematical methods in medicine · 2019Article
- Potential Genes and Pathways of Neonatal Sepsis Based on Functional Gene Set Enrichment Analyses.Computational and mathematical methods in medicine · 2018Article
- Enriched Random Forest for High Dimensional Genomic Data.IEEE/ACM transactions on computational biology and bioinformaticsArticle
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4 authors.
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Abstract
motivationGene set enrichment analyses (GSEAs) are widely used in genomic research to identify underlying biological mechanisms (defined by the gene sets), such as Gene Ontology terms and molecular pathways. There are two caveats in the currently available methods: (i) they are typically designed for group comparisons or regression analyses, which do not utilize temporal information efficiently in time-series of transcriptomics measurements; and (ii) genes overlapping in multiple molecular pathways are considered multiple times in hypothesis testing.
resultsWe propose an inferential framework for GSEA based on functional data analysis, which utilizes the temporal information based on functional principal component analysis, and disentangles the effects of overlapping genes by a functional extension of the elastic-net regression. Furthermore, the hypothesis testing for the gene sets is performed by an extension of Mann-Whitney U test which is based on weighted rank sums computed from correlated observations. By using both simulated datasets and a large-scale time-course gene expression data on human influenza infection, we demonstrate that our method has uniformly better receiver operating characteristic curves, and identifies more pathways relevant to immune-response to human influenza infection than the competing approaches. AVAILABILITY AND IMPLEMENTATION: The methods are implemented in R package FUNNEL, freely and publicly available at: https://github.com/yunzhang813/FUNNEL-GSEA-R-Package . CONTACT: xing_qiu@urmc.rochester.edu or juilee_thakar@urmc.rochester.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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