ArticlePlant physiology2005
Genome cluster database. A sequence family analysis platform for Arabidopsis and rice.
Article in Plant physiology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- Genome-wide identification of members of thePhysiology and molecular biology of plants : an international journal of functional plant biology · 2023Article
- Zinc/iron-regulated transporter-like protein gene family inFrontiers in plant science · 2023Article
- The expansion and diversity of thePeerJ · 2021Article
- Genome-Wide Identification, Sequence Variation, and Expression of the Glycerol-3-Phosphate Acyltransferase (GPAT) Gene Family inFrontiers in genetics · 2019Article
- Phylogenetics and Gene Structure Dynamics of Polygalacturonase Genes in Aspergillus and Neurospora crassa.The plant pathology journal · 2013Article
- SKP1-like-related genes interact with various F-box proteins and may form SCF complexes with Cullin-F-box proteins in wheat.Molecular biology reports · 2013Article
- Phylogenetics and evolution of Su(var)3-9 SET genes in land plants: rapid diversification in structure and function.BMC evolutionary biology · 2011Article
- Phylogenetic and expression analysis of RNA-binding proteins with triple RNA recognition motifs in plants.Molecules and cells · 2011Article
- Genomics and bioinformatics resources for crop improvement.Plant & cell physiology · 2010Review
- PLAZA: a comparative genomics resource to study gene and genome evolution in plants.The Plant cell · 2009Article
- TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics.Plant physiology · 2009Article
- Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes.Genome biology · 2009Article
- Annotating genes of known and unknown function by large-scale coexpression analysis.Plant physiology · 2008Article
- Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants.BMC genomics · 2008Article
- Characterization of paralogous protein families in rice.BMC plant biology · 2008Article
- AffyTrees: facilitating comparative analysis of Affymetrix plant microarray chips.Plant physiology · 2008Article
- Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis.BMC molecular biology · 2008Article
- POGs/PlantRBP: a resource for comparative genomics in plants.Nucleic acids research · 2007Article
- The acyltransferase GPAT5 is required for the synthesis of suberin in seed coat and root of Arabidopsis.The Plant cell · 2007Article
- Biological databases for plant research.Plant physiology · 2005Article
Corrections and comments
- Commented on by
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genome-wide protein sequences from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) spp. japonica were clustered into families using sequence similarity and domain-based clustering. The two fundamentally different methods resulted in separate cluster sets with complementary properties to compensate the limitations for accurate family analysis. Functional names for the identified families were assigned with an efficient computational approach that uses the description of the most common molecular function gene ontology node within each cluster. Subsequently, multiple alignments and phylogenetic trees were calculated for the assembled families. All clustering results and their underlying sequences were organized in the Web-accessible Genome Cluster Database (http://bioinfo.ucr.edu/projects/GCD) with rich interactive and user-friendly sequence family mining tools to facilitate the analysis of any given family of interest for the plant science community. An automated clustering pipeline ensures current information for future updates in the annotations of the two genomes and clustering improvements. The analysis allowed the first systematic identification of family and singlet proteins present in both organisms as well as those restricted to one of them. In addition, the established Web resources for mining these data provide a road map for future studies of the composition and structure of protein families between the two species.
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.