ArticleNucleic acids research2010
Discovering causal signaling pathways through gene-expression patterns.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
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- Leveraging HILIC/ERLIC separations for online nanoscale LC-MS/MS analysis of phosphopeptide isoforms from RNA polymerase II C-terminal domain.Journal of chromatography. B, Analytical technologies in the biomedical and life sciences · 2025Article
- Transcriptome Complexity Disentangled: A Regulatory Molecules Approach.International journal of molecular sciences · 2025Article
- Drug discovery for chemotherapeutic resistance based on pathway-responsive gene sets and its application in breast cancer.Frontiers in bioinformatics · 2025Article
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- The molecular mechanism of sepsis-induced diaphragm dysfunction.Journal of thoracic disease · 2023Article
- Application of perturbation gene expression profiles in drug discovery-From mechanism of action to quantitative modelling.Frontiers in systems biology · 2023Review
- High-fat diet-induced obesity augments the deleterious effects of estrogen deficiency on bone: Evidence from ovariectomized mice.Aging cell · 2022Article
- Bipartite network models to design combination therapies in acute myeloid leukaemia.Nature communications · 2022Article
- Targeting the NANOG/HDAC1 axis reverses resistance to PD-1 blockade by reinvigorating the antitumor immunity cycle.The Journal of clinical investigation · 2022Article
- Identification of hub genes and molecular pathways in human T-lymphotropic virus type 1 associated diseases using protein-protein interactions networks.Iranian journal of microbiology · 2022Article
- Exploring Pathway-Based Group Lasso for Cancer Survival Analysis: A Special Case of Multi-Task Learning.Frontiers in genetics · 2021Article
- Markers of Angiogenesis, Lymphangiogenesis, and Epithelial-Mesenchymal Transition (Plasticity) in CIN and Early Invasive Carcinoma of the Cervix: Exploring Putative Molecular Mechanisms Involved in Early Tumor Invasion.International journal of molecular sciences · 2020Article
- SPEED2: inferring upstream pathway activity from differential gene expression.Nucleic acids research · 2020Article
- The A818-6 system as an in-vitro model for studying the role of the transportome in pancreatic cancer.BMC cancer · 2020Article
- Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data.Genome biology · 2020Article
- Signatures of cell death and proliferation in perturbation transcriptomics data-from confounding factor to effective prediction.Nucleic acids research · 2019Article
- The Signaling Pathways Project, an integrated 'omics knowledgebase for mammalian cellular signaling pathways.Scientific data · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput gene-expression studies result in lists of differentially expressed genes. Most current meta-analyses of these gene lists include searching for significant membership of the translated proteins in various signaling pathways. However, such membership enrichment algorithms do not provide insight into which pathways caused the genes to be differentially expressed in the first place. Here, we present an intuitive approach for discovering upstream signaling pathways responsible for regulating these differentially expressed genes. We identify consistently regulated signature genes specific for signal transduction pathways from a panel of single-pathway perturbation experiments. An algorithm that detects overrepresentation of these signature genes in a gene group of interest is used to infer the signaling pathway responsible for regulation. We expose our novel resource and algorithm through a web server called SPEED: Signaling Pathway Enrichment using Experimental Data sets. SPEED can be freely accessed at http://speed.sys-bio.net/.
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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.