ArticleCurrent genomics2007
Validation of inference procedures for gene regulatory networks.
Article in Current genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Structure Optimization for Large Gene Networks Based on Greedy Strategy.Computational and mathematical methods in medicine · 2018Article
- Semi-Metric Topology of the Human Connectome: Sensitivity and Specificity to Autism and Major Depressive Disorder.PloS one · 2015Article
- Integrated analysis of transcriptomic and proteomic data.Current genomics · 2013Article
- Validation of gene regulatory network inference based on controllability.Frontiers in genetics · 2013Article
- Optimal reference sequence selection for genome assembly using minimum description length principle.EURASIP journal on bioinformatics & systems biology · 2012Article
- On the limitations of biological knowledge.Current genomics · 2012Article
- A statistical approach to selecting and confirming validation targets in -omics experiments.BMC bioinformatics · 2012Article
- Article
- Constraint-based analysis of gene interactions using restricted boolean networks and time-series data.BMC proceedings · 2011Article
- Inference of gene regulatory networks from time series by Tsallis entropy.BMC systems biology · 2011Article
- Inferring Drosophila gap gene regulatory network: pattern analysis of simulated gene expression profiles and stability analysis.BMC research notes · 2009Article
- STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data.BMC bioinformatics · 2009Article
- Inference of gene regulatory networks using time-series data: a survey.Current genomics · 2009Article
- On the long-run sensitivity of probabilistic Boolean networks.Journal of theoretical biology · 2009Article
- On the epistemological crisis in genomics.Current genomics · 2008Article
- Inference of Boolean networks using sensitivity regularization.EURASIP journal on bioinformatics & systems biology · 2008Article
Corrections and comments
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1 author.
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Abstract
The availability of high-throughput genomic data has motivated the development of numerous algorithms to infer gene regulatory networks. The validity of an inference procedure must be evaluated relative to its ability to infer a model network close to the ground-truth network from which the data have been generated. The input to an inference algorithm is a sample set of data and its output is a network. Since input, output, and algorithm are mathematical structures, the validity of an inference algorithm is a mathematical issue. This paper formulates validation in terms of a semi-metric distance between two networks, or the distance between two structures of the same kind deduced from the networks, such as their steady-state distributions or regulatory graphs. The paper sets up the validation framework, provides examples of distance functions, and applies them to some discrete Markov network models. It also considers approximate validation methods based on data for which the generating network is not known, the kind of situation one faces when using real data.
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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.