ArticleBMC biology2005
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release.
Article in BMC biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 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
79 citing papers in PubMed, 195 citations in OpenAlex.
- Engineering carotenoid and steroidal glycoalkaloid depleted tomato fruit for heterologous production of high value terpenes.bioRxiv : the preprint server for biology · 2026Article
- An allelic resolution gene atlas for tetraploid potato provides insights into tuberization and stress resilience.The Plant journal : for cell and molecular biology · 2025Article
- A conceptual framework for human-AI collaborative genome annotation.Briefings in bioinformatics · 2025Review
- Updated Gene Prediction of the Cucumber (9930) Genome through Manual Annotation.Plants (Basel, Switzerland) · 2024Article
- The Arabidopsis Information Resource in 2024.Genetics · 2024Article
- Chromosome-level assembly and analysis of Camelina neglecta: a novel diploid model for Camelina biotechnology research.Biotechnology for biofuels and bioproducts · 2024Article
- Development of Intron Polymorphism Markers and Their Association With Fatty Acid Component Variation in Oil Palm.Frontiers in plant science · 2022Article
- Genomic variation within the maize stiff-stalk heterotic germplasm pool.The plant genome · 2021Article
- Light-regulated pre-mRNA splicing in plants.Current opinion in plant biology · 2021Review
- The tepary bean genome provides insight into evolution and domestication under heat stress.Nature communications · 2021Article
- Proximity to the Promoter and Terminator Regions Regulates the Transcription Enhancement Potential of an Intron.Frontiers in molecular biosciences · 2021Article
- The evolutionary origins of the cat attractant nepetalactone in catnip.Science advances · 2020Article
- Novel intron length polymorphic (ILP) markers from starch biosynthesis genes reveal genetic relationships in Indian wheat varieties and related species.Molecular biology reports · 2020Article
- Genetic Diversity Linked to Haplotype Variation in the World Core Collection ofFrontiers in plant science · 2019Article
- Genome-wide identification of the pectate lyase-like (PLL) gene family and functional analysis of two PLL genes in rice.Molecular genetics and genomics : MGG · 2018Article
- Methodological bias associated with soluble protein recovery from soil.Scientific reports · 2018Article
- Architecture and Distribution of Introns in Core Genes of FourG3 (Bethesda, Md.) · 2017Article
- Article
- Article
- Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application).BMC bioinformatics · 2013Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSince the initial publication of its complete genome sequence, Arabidopsis thaliana has become more important than ever as a model for plant research. However, the initial genome annotation was submitted by multiple centers using inconsistent methods, making the data difficult to use for many applications.
resultsOver the course of three years, TIGR has completed its effort to standardize the structural and functional annotation of the Arabidopsis genome. Using both manual and automated methods, Arabidopsis gene structures were refined and gene products were renamed and assigned to Gene Ontology categories. We present an overview of the methods employed, tools developed, and protocols followed, summarizing the contents of each data release with special emphasis on our final annotation release (version 5).
conclusionOver the entire period, several thousand new genes and pseudogenes were added to the annotation. Approximately one third of the originally annotated gene models were significantly refined yielding improved gene structure annotations, and every protein-coding gene was manually inspected and classified using Gene Ontology terms.
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.