ReviewDatabase : the journal of biological databases and curation2015
Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges.
Review in Database : the journal of biological databases and curation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 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.
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Who cites it
63 citing papers in PubMed.
- Unraveling cell-cell communication through spatial transcriptomics: a review of computational methods.Briefings in bioinformatics · 2026Review
- The allostery principle supports the symbolic character of signaling circuits: gene regulation provides a form of intelligence to living systems.Theory in biosciences = Theorie in den Biowissenschaften · 2026Article
- Caspofungin enhances antifungal immunity in human blood through transcriptional reprogramming.microLife · 2026Article
- Critical analysis of descriptive microRNA data in the translational research on cardioprotection and cardiac repair: lost in the complexity of bioinformatics.Basic research in cardiology · 2025Review
- A workflow for human health hazard evaluation using transcriptomic data and Key Characteristics-based gene sets.Toxicological sciences : an official journal of the Society of Toxicology · 2025Article
- STCDB4ND: a signal transduction classification database for neurological diseases.Database : the journal of biological databases and curation · 2025Article
- Advances and challenges in cell-cell communication inference: a comprehensive review of tools, resources, and future directions.Briefings in bioinformatics · 2025Review
- Overview and limitations of database in global traditional medicines: A narrative review.Acta pharmacologica Sinica · 2025Review
- Pathway-guided architectures for interpretable AI in biological research.Computational and structural biotechnology journal · 2025Review
- A Computational Protocol for the Knowledge-Based Assessment and Capture of Pathologies.Methods in molecular biology (Clifton, N.J.) · 2025Article
- PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration.PLoS computational biology · 2024Article
- PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration.bioRxiv : the preprint server for biology · 2024Article
- Multiomics of Tissue Extracellular Vesicles Identifies Unique Modulators of Atherosclerosis and Calcific Aortic Valve Stenosis.Circulation · 2023Article
- Omics and systems view of innate immune pathways.Proteomics · 2023Review
- Benchmarking causal reasoning algorithms for gene expression-based compound mechanism of action analysis.BMC bioinformatics · 2023Article
- Mechanism and Therapeutic Prospect of miRNAs in Neurodegenerative Diseases.Behavioural neurology · 2023Review
- SynDISCO: A Mechanistic Modeling-Based Framework for Predictive Prioritization of Synergistic Drug Combinations Targeting Cell Signalling Networks.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.Briefings in bioinformatics · 2022Article
- Article
- Discrete modeling for integration and analysis of large-scale signaling networks.PLoS computational biology · 2022Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Elucidating the complexities of cell signaling pathways is of immense importance to gain understanding about various biological phenomenon, such as dynamics of gene/protein expression regulation, cell fate determination, embryogenesis and disease progression. The successful completion of human genome project has also helped experimental and theoretical biologists to analyze various important pathways. To advance this study, during the past two decades, systematic collections of pathway data from experimental studies have been compiled and distributed freely by several databases, which also integrate various computational tools for further analysis. Despite significant advancements, there exist several drawbacks and challenges, such as pathway data heterogeneity, annotation, regular update and automated image reconstructions, which motivated us to perform a thorough review on popular and actively functioning 24 cell signaling databases. Based on two major characteristics, pathway information and technical details, freely accessible data from commercial and academic databases are examined to understand their evolution and enrichment. This review not only helps to identify some novel and useful features, which are not yet included in any of the databases but also highlights their current limitations and subsequently propose the reasonable solutions for future database development, which could be useful to the whole scientific community.
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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.