The TIGR Rice Genome Annotation Resource: improvements and new features

By S. Ouyang, Wei Zhu, John A. Hamilton, Haining Lin, Matthew A. Campbell, K. Childs, Françoise Thibaud-Nissen, R. Malek, Yuandan Lee, Li Zheng and 4 more. Nucleic Acids Res., 2006

1,209 citations recorded by the source corpus.

In The Institute for Genomic Research Rice Genome Annotation project (), we have continued to update the rice genome sequence with new data and improve the quality of the annotation. In our current release of annotation (Release 4.0; January 12, 2006), we have identified 42 653 non-transposable element-related genes encoding 49 472 gene models as a result of the detection of alternative splicing. We have refined our identification methods for transposable element-related genes resulting in 13 237 genes that are related to transposable elements. Through incorporation of multiple transcript and proteomic expression data sets, we have been able to annotate 24 799 genes (31 739 gene models), representing ∼50% of the total gene models, as expressed in the rice genome. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 59 tracks. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/674b2eb367c83001d807b8f42f94b4b621345146

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

In Plant Science

Citations in the corpus

PsRobot: a web-based plant small RNA meta-analysis toolbox (2012, methodology): “The Arabidopsis thaliana genome was downloaded from the Arabidopsis Information Resource (TAIR) (24) and the rice genome was from Rice Genome Annotation Project (RGAP) (25) and the Rice Annotation Project Database (RAP-DB) (26) databases.”
Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica) (2010, neutral): “1 (Ouyang et al., 2007).”
SyMAP v3.4: a turnkey synteny system with application to plant genomes (2011, background): “In the following, results from comparing the sequenced genomes of rice (37,38), sorghum (39) and maize (40) using SyMAP are discussed; this is not intended to be a robust coverage of the evolutionary events for these plants, but only as a way to illustrate the processing and types of information tha”
expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform1[OPEN] (2016, methodology): “This problem is also exemplified in more mature systems such as rice, where two different genome annotations are widely used: Rice Annotation Project gene models and Michigan State University gene models (Ohyanagi et al., 2006; Ouyang et al., 2007).”
QuantPrime – a flexible tool for reliable high-throughput primer design for quantitative PCR (2008, background): “Oryza sativa ssp japonica Yes Yes Yes TIGR release 5 [29]”
Germins: A diverse protein family important for crop improvement (2009, background): “Two additional data sources were used for the rice germins, the Massively Parallel Signature Sequencing (MPSS) Rice Expression Atlas (http:// mpss.udel.edu/rice/; University of Delaware [44] and the Rice Genome Annotation Digital Northern database (http://rice.plantbiology.msu.edu/dnav.shtml; Michig”
Phytozome: a comparative platform for green plant genomics (2011, background): “0 (18) Physcomitrella patens Moss JGI assembly v1.”
Genomewide SNP variation reveals relationships among landraces and modern varieties of rice (2009, methodology): “For the MBMLintersect SNP set, a total of 158,928 of 159,879 IRGSP localized SNPs were mapped to the TIGR pseudomolecules.”
starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data (2010, methodology): “Rice genome sequences were downloaded from the MSU Rice Genome Annotation Website (43).”
Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics (2013, neutral): “Project (Ouyang et al. 2007); this latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.”
Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. (2014, background): “2012), ∼57 000 rice proteins (Ouyang et al. 2007), ∼17 000 Chlamydomonas reinhardtii protein models (Merchant et al.”
agriGO: a GO analysis toolkit for the agricultural community (2010, background): “With rice for example, available background includes TIGR (14) and Gramene (15) genes, KOME (16) full-length cDNAs and microarray probe (set) IDs from Aﬀymetrix (www.aﬀymetrix.com), Agilent (www.agilent.com), BGI (www.genomics.org.cn) and other platforms.”