ArticleNucleic acids research2020
SPEED2: inferring upstream pathway activity from differential gene expression.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
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27 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Comprehensive Integration of Genome-Wide Association and Gene Expression Studies Reveals Novel Gene Signatures and Potential Therapeutic Targets forFrontiers in immunology · 2021Pooled it
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- Inferring pathway activity from single-cell and spatial transcriptomics data with PaaSc.PLoS computational biology · 2025Article
- Exploring the molecular mechanism ofHeliyon · 2025Article
- Exploration of telomere-related biomarkers for lung adenocarcinoma and targeted drug prediction.Discover oncology · 2025Article
- Drug discovery for chemotherapeutic resistance based on pathway-responsive gene sets and its application in breast cancer.Frontiers in bioinformatics · 2025Article
- Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system.Nature immunology · 2024Review
- Bronchial epithelial transcriptomics and experimental validation reveal asthma severity-related neutrophilc signatures and potential treatments.Communications biology · 2024Article
- Time-of-day-dependent variation of the human liver transcriptome and metabolome is disrupted in MASLD.JHEP reports : innovation in hepatology · 2024Article
- Combination of tumor asphericity and an extracellular matrix-related prognostic gene signature in non-small cell lung cancer patients.Scientific reports · 2023Article
- Neurodevelopmental disorders and cancer networks share pathways, but differ in mechanisms, signaling strength, and outcome.NPJ genomic medicine · 2023Article
- Glucocorticoid activation of anti-inflammatory macrophages protects against insulin resistance.Nature communications · 2023Article
- Antineoplastic Nature ofBiology · 2023Article
- Study of kaempferol in the treatment of COVID-19 combined with Chikungunya co-infection by network pharmacology and molecular docking technology.Informatics in medicine unlocked · 2023Article
- Application of perturbation gene expression profiles in drug discovery-From mechanism of action to quantitative modelling.Frontiers in systems biology · 2023Review
- Quercetin is a Potential Therapy for Rheumatoid Arthritis via Targeting Caspase-8 Through Ferroptosis and Pyroptosis.Journal of inflammation research · 2023Article
- Insights into potential mechanisms of asthma patients with COVID-19: A study based on the gene expression profiling of bronchoalveolar lavage fluid.Computers in biology and medicine · 2022Article
- SARS-CoV-2 induces "cytokine storm" hyperinflammatory responses in RA patients through pyroptosis.Frontiers in immunology · 2022Article
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4 authors.
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Abstract
Extracting signalling pathway activities from transcriptome data is important to infer mechanistic origins of transcriptomic dysregulation, for example in disease. A popular method to do so is by enrichment analysis of signature genes in e.g. differentially regulated genes. Previously, we derived signatures for signalling pathways by integrating public perturbation transcriptome data and generated a signature database called SPEED (Signalling Pathway Enrichment using Experimental Datasets), for which we here present a substantial upgrade as SPEED2. This web server hosts consensus signatures for 16 signalling pathways that are derived from a large number of transcriptomic signalling perturbation experiments. When providing a gene list of e.g. differentially expressed genes, the web server allows to infer signalling pathways that likely caused these genes to be deregulated. In addition to signature lists, we derive 'continuous' gene signatures, in a transparent and automated fashion without any fine-tuning, and describe a new algorithm to score these signatures.
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