ArticleNucleic acids research2018
PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed.
- GOLDEN fusion: a graph-oriented learning with domain-embedding network fusion for generating super gene sets in functional genomics.Briefings in bioinformatics · 2026Article
- Temporal GeneTerrain: advancing precision medicine through dynamic gene expression visualization.Frontiers in bioinformatics · 2025Article
- GETgene-AI: a framework for prioritizing actionable cancer drug targets.Frontiers in systems biology · 2025Article
- PAGER-scFGA: unveiling cell functions and molecular mechanisms in cell trajectories through single-cell functional genomics analysis.Frontiers in bioinformatics · 2024Article
- Analysis of cardiac single-cell RNA-sequencing data can be improved by the use of artificial-intelligence-based tools.Scientific reports · 2023Article
- Neuroendocrine signaling in the skin with a special focus on the epidermal neuropeptides.American journal of physiology. Cell physiology · 2022Review
- DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features.Bioinformatics (Oxford, England) · 2022Article
- TUBB4A interacts with MYH9 to protect the nucleus during cell migration and promotes prostate cancer via GSK3β/β-catenin signalling.Nature communications · 2022Article
- A nonredundant role for T cell-derived interleukin 22 in antibacterial defense of colonic crypts.Immunity · 2022Article
- MVIP: multi-omics portal of viral infection.Nucleic acids research · 2022Article
- WINNER: A network biology tool for biomolecular characterization and prioritization.Frontiers in big data · 2022Article
- PAGER Web APP: An Interactive, Online Gene Set and Network Interpretation Tool for Functional Genomics.Frontiers in genetics · 2022Article
- Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical exams.BMC medical informatics and decision making · 2021Article
- PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies.Nucleic acids research · 2021Article
- Biological Network Mining.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Association study based on topological constraints of protein-protein interaction networks.Scientific reports · 2020Article
- WIPER: Weighted in-Path Edge Ranking for biomolecular association networks.Quantitative biology (Beijing, China) · 2019Article
- BEERE: a web server for biomedical entity expansion, ranking and explorations.Nucleic acids research · 2019Article
- "Super Gene Set" Causal Relationship Discovery from Functional Genomics Data.IEEE/ACM transactions on computational biology and bioinformaticsArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Integrative Gene-set, Network and Pathway Analysis (GNPA) is a powerful data analysis approach developed to help interpret high-throughput omics data. In PAGER 1.0, we demonstrated that researchers can gain unbiased and reproducible biological insights with the introduction of PAGs (Pathways, Annotated-lists and Gene-signatures) as the basic data representation elements. In PAGER 2.0, we improve the utility of integrative GNPA by significantly expanding the coverage of PAGs and PAG-to-PAG relationships in the database, defining a new metric to quantify PAG data qualities, and developing new software features to simplify online integrative GNPA. Specifically, we included 84 282 PAGs spanning 24 different data sources that cover human diseases, published gene-expression signatures, drug-gene, miRNA-gene interactions, pathways and tissue-specific gene expressions. We introduced a new normalized Cohesion Coefficient (nCoCo) score to assess the biological relevance of genes inside a PAG, and RP-score to rank genes and assign gene-specific weights inside a PAG. The companion web interface contains numerous features to help users query and navigate the database content. The database content can be freely downloaded and is compatible with third-party Gene Set Enrichment Analysis tools. We expect PAGER 2.0 to become a major resource in integrative GNPA. PAGER 2.0 is available at http://discovery.informatics.uab.edu/PAGER/.
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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.