ArticleCommunications biology2018
2D association and integrative omics analysis in rice provides systems biology view in trait analysis.
Article in Communications biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 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
4 citing papers in PubMed.
- Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice.Rice (New York, N.Y.) · 2023Article
- PIP-SNP: a pipeline for processing SNP data featured as linkage disequilibrium bin mapping, genotype imputing and marker synthesizing.NAR genomics and bioinformatics · 2021Article
- Distinguishing HapMap Accessions Through Recursive Set Partitioning in Hierarchical Decision Trees.Frontiers in plant science · 2021Article
- GPU empowered pipelines for calculating genome-wide kinship matrices with ultra-high dimensional genetic variants and facilitating 1D and 2D GWAS.NAR genomics and bioinformatics · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The interactions among genes and between genes and environment contribute significantly to the phenotypic variation of complex traits and may be possible explanations for missing heritability. However, to our knowledge no existing tool can address the two kinds of interactions. Here we propose a novel linear mixed model that considers not only the additive effects of biological markers but also the interaction effects of marker pairs. Interaction effect is demonstrated as a 2D association. Based on this linear mixed model, we developed a pipeline, namely PATOWAS. PATOWAS can be used to study transcriptome-wide and metabolome-wide associations in addition to genome-wide associations. Our case analysis with real rice recombinant inbred lines (RILs) at three omics levels demonstrates that 2D association mapping and integrative omics are able to provide a systems biology view into the analyzed traits, leading toward an answer about how genes, transcripts, proteins, and metabolites work together to produce an observable phenotype.
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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.