ArticleBioinformatics (Oxford, England)2015
PAGER: constructing PAGs and new PAG-PAG relationships for network biology.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 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
- Mondrian Abstraction and Language Model Embeddings for Differential Pathway Analysis.bioRxiv : the preprint server for biology · 2024Article
- Explorative Discovery of Gene Signatures and Clinotypes in Glioblastoma Cancer Through GeneTerrain Knowledge Map Representation.bioRxiv : the preprint server for biology · 2024Article
- 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
- An in vivo model of glioblastoma radiation resistance identifies long noncoding RNAs and targetable kinases.JCI insight · 2022Article
- DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features.Bioinformatics (Oxford, England) · 2022Article
- A nonredundant role for T cell-derived interleukin 22 in antibacterial defense of colonic crypts.Immunity · 2022Article
- PAGER Web APP: An Interactive, Online Gene Set and Network Interpretation Tool for Functional Genomics.Frontiers in genetics · 2022Article
- WINNER: A network biology tool for biomolecular characterization and prioritization.Frontiers in big data · 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
- Cancer Explant Models.Current topics in microbiology and immunology · 2021Article
- Biological Network Mining.Methods in molecular biology (Clifton, N.J.) · 2021Article
- WIPER: Weighted in-Path Edge Ranking for biomolecular association networks.Quantitative biology (Beijing, China) · 2019Article
- PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology.Nucleic acids research · 2018Article
- Repositioning drugs by targeting network modules: a Parkinson's disease case study.BMC bioinformatics · 2017Article
- A method for developing regulatory gene set networks to characterize complex biological systems.BMC genomics · 2015Article
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Authors and funding
8 authors.
Funding
Abstract
In this article, we described a new database framework to perform integrative "gene-set, network, and pathway analysis" (GNPA). In this framework, we integrated heterogeneous data on pathways, annotated list, and gene-sets (PAGs) into a PAG electronic repository (PAGER). PAGs in the PAGER database are organized into P-type, A-type and G-type PAGs with a three-letter-code standard naming convention. The PAGER database currently compiles 44 313 genes from 5 species including human, 38 663 PAGs, 324 830 gene-gene relationships and two types of 3 174 323 PAG-PAG regulatory relationships-co-membership based and regulatory relationship based. To help users assess each PAG's biological relevance, we developed a cohesion measure called Cohesion Coefficient (CoCo), which is capable of disambiguating between biologically significant PAGs and random PAGs with an area-under-curve performance of 0.98. PAGER database was set up to help users to search and retrieve PAGs from its online web interface. PAGER enable advanced users to build PAG-PAG regulatory networks that provide complementary biological insights not found in gene set analysis or individual gene network analysis. We provide a case study using cancer functional genomics data sets to demonstrate how integrative GNPA help improve network biology data coverage and therefore biological interpretability. The PAGER database can be accessible openly at http://discovery.informatics.iupui.edu/PAGER/.
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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.