ArticlePLoS computational biology2013
Differential expression analysis for pathways.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 35 papers, 1 of them a synthesis that pooled it.
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Who cites it
35 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Identification of shared genetic architecture between non-alcoholic fatty liver disease and type 2 diabetes: A genome-wide analysis.Frontiers in endocrinology · 2023Pooled it
- Longitudinal omics data analysis: approaches and applications.Computational and structural biotechnology journal · 2026Review
- DRaCOon: a novel algorithm for pathway-level differential co-expression analysis in transcriptomics.BMC bioinformatics · 2025Article
- A gene pathway enrichment method based on improved TF-IDF algorithm.Biochemistry and biophysics reports · 2023Article
- Integrating knowledge and omics to decipher mechanisms via large-scale models of signaling networks.Molecular systems biology · 2022Review
- Applications and Challenges of Machine Learning Methods in Alzheimer's Disease Multi-Source Data Analysis.Current genomics · 2021Review
- Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data.Computational and structural biotechnology journal · 2021Article
- Discovery of a transcriptomic core of genes shared in 8 primary retinoblastoma with a novel detection score analysis.Journal of cancer research and clinical oncology · 2020Article
- Transcriptome profiling reveals insertional mutagenesis suppressed the expression of candidate pathogenicity genes in honeybee fungal pathogen, Ascosphaera apis.Scientific reports · 2020Article
- Integrated, multicohort analysis reveals unified signature of systemic lupus erythematosus.JCI insight · 2020Article
- A comparison of mechanistic signaling pathway activity analysis methods.Briefings in bioinformatics · 2019Review
- Single-cell technologies in reproductive immunology.American journal of reproductive immunology (New York, N.Y. : 1989) · 2019Review
- Arsenic Reduces Gene Expression Response to Changing Salinity in Killifish.Environmental science & technology · 2018Article
- SPSNet: subpopulation-sensitive network-based analysis of heterogeneous gene expression data.BMC systems biology · 2018Article
- Transcriptome and Cell Physiological Analyses in Different Rice Cultivars Provide New Insights Into Adaptive and Salinity Stress Responses.Frontiers in plant science · 2018Article
- Internal driving factors leading to extrahepatic manifestation of the hepatitis C virus infection.International journal of molecular medicine · 2017Article
- sPAGM: inferring subpathway activity by integrating gene and miRNA expression-robust functional signature identification for melanoma prognoses.Scientific reports · 2017Article
- Androgen receptor-deficient islet β-cells exhibit alteration in genetic markers of insulin secretion and inflammation. A transcriptome analysis in the male mouse.Journal of diabetes and its complications · 2017Article
- Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms.Bioinformatics (Oxford, England) · 2017Article
- High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes.Oncotarget · 2017Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
Abstract
Life science technologies generate a deluge of data that hold the keys to unlocking the secrets of important biological functions and disease mechanisms. We present DEAP, Differential Expression Analysis for Pathways, which capitalizes on information about biological pathways to identify important regulatory patterns from differential expression data. DEAP makes significant improvements over existing approaches by including information about pathway structure and discovering the most differentially expressed portion of the pathway. On simulated data, DEAP significantly outperformed traditional methods: with high differential expression, DEAP increased power by two orders of magnitude; with very low differential expression, DEAP doubled the power. DEAP performance was illustrated on two different gene and protein expression studies. DEAP discovered fourteen important pathways related to chronic obstructive pulmonary disease and interferon treatment that existing approaches omitted. On the interferon study, DEAP guided focus towards a four protein path within the 26 protein Notch signalling pathway.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.