ArticleGenomics, proteomics & bioinformatics2020
IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data.
Article in Genomics, proteomics & bioinformatics, 2020. 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.
- Comparative transcriptome analysis reveals key genes and regulatory networks regulating flowering in rice varieties with different photoperiod sensitivity.BMC plant biology · 2026Article
- Rice Annotation Project Database (RAP-DB): Literature-Curated Gene Annotation and Integrated Omics Resources for Rice Functional Genomics and Molecular Breeding.Rice (New York, N.Y.) · 2026Article
- Identification of universal grass genes and estimates of their monocot-/commelinid-/grass-specificity.Bioinformatics advances · 2025Article
- Characterization and Transcriptomic Analysis of Sorghum EIN/EIL Family and Identification of Their Roles in Internode Maturation.Plants (Basel, Switzerland) · 2024Article
- Potential Roles of the GRF Transcription Factors in Sorghum Internodes during Post-Reproductive Stages.Plants (Basel, Switzerland) · 2024Article
- Divergent Roles of the Auxin Response Factors in Lemongrass (International journal of molecular sciences · 2024Article
- Updated Gene Prediction of the Cucumber (9930) Genome through Manual Annotation.Plants (Basel, Switzerland) · 2024Article
- Plant genomic resources at National Genomics Data Center: assisting in data-driven breeding applications.aBIOTECH · 2024Review
- Article
- MDSi: Multi-omics Database for Setaria italica.BMC plant biology · 2023Article
- GWAS Atlas: an updated knowledgebase integrating more curated associations in plants and animals.Nucleic acids research · 2023Article
- Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels.Nucleic acids research · 2022Article
- Genomics and transcriptomics to protect rice (Frontiers in plant science · 2022Review
- RiceLncPedia: a comprehensive database of rice long non-coding RNAs.Plant biotechnology journal · 2021Article
- Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Review
- Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021.Nucleic acids research · 2021Article
- Genome Variation Map: a worldwide collection of genome variations across multiple species.Nucleic acids research · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function. Although the availability of massive RNA-seq data provides great opportunities for gene model refinement, few efforts have been made to adopt these precious data in rice genome reannotation. Here we reannotate the rice (Oryza sativa L. ssp. japonica) genome based on integration of large-scale RNA-seq data and release a new annotation system IC4R-2.0. In general, IC4R-2.0 significantly improves the completeness of gene structure, identifies a number of novel genes, and integrates a variety of functional annotations. Furthermore, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are systematically characterized in the rice genome. Performance evaluation shows that compared to previous annotation systems, IC4R-2.0 achieves higher integrity and quality, primarily attributable to massive RNA-seq data applied in genome annotation. Consequently, we incorporate the improved annotations into the Information Commons for Rice (IC4R), a database integrating multiple omics data of rice, and accordingly update IC4R by providing more user-friendly web interfaces and implementing a series of practical online tools. Together, the updated IC4R, which is equipped with the improved annotations, bears great promise for comparative and functional genomic studies in rice and other monocotyledonous species. The IC4R-2.0 annotation system and related resources are freely accessible at http://ic4r.org/.
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.