ArticlePloS one2012
PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
17 citing papers in PubMed.
- Evidence that variation in root anatomy contributes to local adaptation in Mexican native maize.Evolutionary applications · 2024Article
- Synchronization of senescence and desynchronization of flowering inAoB PLANTS · 2020Article
- SNP variable selection by generalized graph domination.PloS one · 2019Article
- A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice (International journal of molecular sciences · 2018Article
- Prioritising candidate genes causing QTL using hierarchical orthologous groups.Bioinformatics (Oxford, England) · 2018Article
- Association Mapping of Flowering and Height Traits in Germplasm Enhancement of Maize Doubled Haploid (GEM-DH) Lines.The plant genome · 2018Article
- Gramene 2018: unifying comparative genomics and pathway resources for plant research.Nucleic acids research · 2018Article
- Transcriptome Analysis of Flowering Time Genes under Drought Stress in Maize Leaves.Frontiers in plant science · 2017Article
- A comprehensive study of the genomic differentiation between temperate Dent and Flint maize.Genome biology · 2016Article
- Temporal Shift of Circadian-Mediated Gene Expression and Carbon Fixation Contributes to Biomass Heterosis in Maize Hybrids.PLoS genetics · 2016Article
- A Meta-Analysis Based Method for Prioritizing Candidate Genes Involved in a Pre-specific Function.Frontiers in plant science · 2016Article
- Prioritization of candidate genes in "QTL-hotspot" region for drought tolerance in chickpea (Cicer arietinum L.).Scientific reports · 2015Article
- Shared Genomic Regions Between Derivatives of a Large Segregating Population of Maize Identified Using Bulked Segregant Analysis Sequencing and Traditional Linkage Analysis.G3 (Bethesda, Md.) · 2015Article
- Genetic dissection of ozone tolerance in rice (Oryza sativa L.) by a genome-wide association study.Journal of experimental botany · 2015Article
- Prioritization of candidate genes in QTL regions based on associations between traits and biological processes.BMC plant biology · 2014Article
- Insights into the maize pan-genome and pan-transcriptome.The Plant cell · 2014Article
- Getting to the roots of it: Genetic and hormonal control of root architecture.Frontiers in plant science · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
PICARA is an analytical pipeline designed to systematically summarize observed SNP/trait associations identified by genome wide association studies (GWAS) and to identify candidate genes involved in the regulation of complex trait variation. The pipeline provides probabilistic inference about a priori candidate genes using integrated information derived from genome-wide association signals, gene homology, and curated gene sets embedded in pathway descriptions. In this paper, we demonstrate the performance of PICARA using data for flowering time variation in maize - a key trait for geographical and seasonal adaption of plants. Among 406 curated flowering time-related genes from Arabidopsis, we identify 61 orthologs in maize that are significantly enriched for GWAS SNP signals, including key regulators such as FT (Flowering Locus T) and GI (GIGANTEA), and genes centered in the Arabidopsis circadian pathway, including TOC1 (Timing of CAB Expression 1) and LHY (Late Elongated Hypocotyl). In addition, we discover a regulatory feature that is characteristic of these a priori flowering time candidates in maize. This new probabilistic analytical pipeline helps researchers infer the functional significance of candidate genes associated with complex traits and helps guide future experiments by providing statistical support for gene candidates based on the integration of heterogeneous biological information.
Indexed as
Identifiers
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.