ArticleGenomics
Inference and validation of predictive gene networks from biomedical literature and gene expression data.
Article in Genomics. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers, 1 of them a synthesis that pooled it.
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
14 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systems Genetics Analysis of Genome-Wide Association Study Reveals Novel Associations Between Key Biological Processes and Coronary Artery Disease.Arteriosclerosis, thrombosis, and vascular biology · 2015Pooled it
- Article
- WINNER: A network biology tool for biomolecular characterization and prioritization.Frontiers in big data · 2022Article
- Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms.Scientific reports · 2020Article
- RGBM: regularized gradient boosting machines for identification of the transcriptional regulators of discrete glioma subtypes.Nucleic acids research · 2018Article
- Construction and analysis of gene-gene dynamics influence networks based on a Boolean model.BMC systems biology · 2017Article
- Analytical Strategy to Prioritize Alzheimer's Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data.Journal of Alzheimer's disease : JAD · 2017Article
- Inferring causal molecular networks: empirical assessment through a community-based effort.Nature methods · 2016Article
- Systems Biology Approaches for Host-Fungal Interactions: An Expanding Multi-Omics Frontier.Omics : a journal of integrative biology · 2016Review
- Taking Bioinformatics to Systems Medicine.Methods in molecular biology (Clifton, N.J.) · 2016Review
- Using shRNA experiments to validate gene regulatory networks.Genomics data · 2015Article
- Article
- Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks.Frontiers in cell and developmental biology · 2014Review
- Relevance of different prior knowledge sources for inferring gene interaction networks.Frontiers in genetics · 2014Article
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
Although many methods have been developed for inference of biological networks, the validation of the resulting models has largely remained an unsolved problem. Here we present a framework for quantitative assessment of inferred gene interaction networks using knock-down data from cell line experiments. Using this framework we are able to show that network inference based on integration of prior knowledge derived from the biomedical literature with genomic data significantly improves the quality of inferred networks relative to other approaches. Our results also suggest that cell line experiments can be used to quantitatively assess the quality of networks inferred from tumor samples.
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What OpenQuestion holds
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.