ArticleGenetics2013
Modeling causality for pairs of phenotypes in system genetics.
Article in Genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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Who cites it
21 citing papers in PubMed, 39 citations in OpenAlex.
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- The trouble with triples: Examining the impact of measurement error in mediation analysis.Genetics · 2023Article
- Lipidomic QTL in Diversity Outbred mice identifies a novel function for α/β hydrolase domain 2 (bioRxiv : the preprint server for biology · 2023Article
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- Genetic determinants of gut microbiota composition and bile acid profiles in mice.PLoS genetics · 2019Article
- Gene loci associated with insulin secretion in islets from non-diabetic mice.The Journal of clinical investigation · 2019Article
- Risk-modeling of dog osteosarcoma genome scans shows individuals with Mendelian-level polygenic risk are common.BMC genomics · 2019Article
- High-Dimensional Bayesian Network Inference From Systems Genetics Data Using Genetic Node Ordering.Frontiers in genetics · 2019Article
- Learning Causal Biological Networks With the Principle of Mendelian Randomization.Frontiers in genetics · 2019Article
- Temporal genetic association and temporal genetic causality methods for dissecting complex networks.Nature communications · 2018Article
- Genetic Drivers of Pancreatic Islet Function.Genetics · 2018Article
- C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis.PLoS computational biology · 2017Article
- Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data.PLoS computational biology · 2017Article
- Next Generation Mapping of Enological Traits in an F2 Interspecific Grapevine Hybrid Family.PloS one · 2016Article
- Bayesian network reconstruction using systems genetics data: comparison of MCMC methods.Genetics · 2015Article
- Article
- Mapping eQTL networks with mixed graphical Markov models.Genetics · 2014Article
- Novel distal eQTL analysis demonstrates effect of population genetic architecture on detecting and interpreting associations.Genetics · 2014Article
- JOINT ANALYSIS OF SNP AND GENE EXPRESSION DATA IN GENETIC ASSOCIATION STUDIES OF COMPLEX DISEASES.The annals of applied statistics · 2014Article
- Interrogating causal pathways linking genetic variants, small molecule metabolites, and circulating lipids.Genome medicine · 2014Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Current efforts in systems genetics have focused on the development of statistical approaches that aim to disentangle causal relationships among molecular phenotypes in segregating populations. Reverse engineering of transcriptional networks plays a key role in the understanding of gene regulation. However, transcriptional regulation is only one possible mechanism, as methylation, phosphorylation, direct protein-protein interaction, transcription factor binding, etc., can also contribute to gene regulation. These additional modes of regulation can be interpreted as unobserved variables in the transcriptional gene network and can potentially affect its reconstruction accuracy. We develop tests of causal direction for a pair of phenotypes that may be embedded in a more complicated but unobserved network by extending Vuong's selection tests for misspecified models. Our tests provide a significance level, which is unavailable for the widely used AIC and BIC criteria. We evaluate the performance of our tests against the AIC, BIC, and a recently published causality inference test in simulation studies. We compare the precision of causal calls using biologically validated causal relationships extracted from a database of 247 knockout experiments in yeast. Our model selection tests are more precise, showing greatly reduced false-positive rates compared to the alternative approaches. In practice, this is a useful feature since follow-up studies tend to be time consuming and expensive and, hence, it is important for the experimentalist to have causal predictions with low false-positive rates.
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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.