Functional Annotation of the Arabidopsis Genome Using Controlled Vocabularies1

By T. Berardini, S. Mundodi, L. Reiser, E. Huala, M. Garcia-Hernandez, Peifen Zhang, Lukas A. Mueller, J. Yoon, Aisling Doyle, Gabriel Lander and 8 more. Plant Physiology, 2004

469 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/12a4ed6a8337bd83c7e53478a177f1aa967f908f

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Citations in the corpus

Striking Similarities in the Genomic Distribution of Tandemly Arrayed Genes in Arabidopsis and Rice (2006, methodology): “We used plant-related GO Slim terms [51], as of 1 April 2005, to explore TAG functions.”
The use of microarray μPEACH1.0 to investigate transcriptome changes during transition from pre-climacteric to climacteric phase in peach fruit (2006, methodology): “Genes showing log2 ratio >1 (up-regulated) and 1 (down-regulated) were annotated following the Gene Ontology categories (GO) developed by TAIR [17].”
The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses (2012, methodology): “Arabidopsis annotations to GO terms are developed by the TAIR (Berardini et al. 2004, Lamesch et al. 2012) through their curation pipeline and are added to the PO database at each PO release through an automated pull process from the GO FTP site (ftp://ftp.geneontology.org/pub/go/gene…”
The Arabidopsis Information Resource: Making and Mining the ‘Gold Standard’ Annotated Reference Plant Genome (2015, background): “Curated data include, but are not limited to, gene function information captured in the form of Gene Ontology (GO) annotations (Berardini et al ., 2004; Gene Ontology Consortium et al ., 2013), gene expression information in the form of Plant Ontology (PO) annotations (Cooper et al ., 2013), gene…”
RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome (2010, methodology): “The Arabidopsis gene model of estimated best fit was then connected to the concurrent gene ontology [32].”
The xenobiotic β‐aminobutyric acid enhances Arabidopsis thermotolerance (2008, background): “Table S1 by molecular function (Figure 3) (Berardini et al., 2004).”
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis (2006, methodology): “(iv) A functional category page is constructed for each gene function category using the 3481 terms defined by GO (21), KEGG (22), AraCyc (23) and KaPPA-View (24).”
Proteome profile and functional classification of proteins in Arabidopsis thaliana (Landsberg erecta) mature pollen (2006, methodology): “Using the Gene Ontology annotation for Arabidopsis (Berardini et al. 2004), the relative distribution of identified proteins (Table 1) associated with various cell components is presented in Fig.”