MODOMICS: a database of RNA modification pathways. 2008 update
By Anna Czerwoniec, Stanislaw Dunin-Horkawicz, Elżbieta Purta, Katarzyna H. Kaminska, Joanna M. Kasprzak, Janusz M. Bujnicki, Henri Grosjean, Kristian Rother. Nucleic Acids Research, 2008
1,116 citations recorded by the source corpus.
MODOMICS, a database devoted to the systems biology of RNA modification, has been subjected to substantial improvements. It provides comprehensive information on the chemical structure of modified nucleosides, pathways of their biosynthesis, sequences of RNAs containing these modifications and RNA-modifying enzymes. MODOMICS also provides cross-references to other databases and to literature. In addition to the previously available manually curated tRNA sequences from a few model organisms, we have now included additional tRNAs and rRNAs, and all RNAs with 3D structures in the Nucleic Acid Database, in which modified nucleosides are present. In total, 3460 modified bases in RNA sequences of different organisms have been annotated. New RNA-modifying enzymes have been also added. The current collection of enzymes includes mainly proteins for the model organisms Escherichia coli and Saccharomyces cerevisiae, and is currently being expanded to include proteins from other organisms, in particular Archaea and Homo sapiens. For enzymes with known structures, links are provided to the corresponding Protein Data Bank entries, while for many others homology models have been created. Many new options for database searching and querying have been included. MODOMICS can be accessed at http://genesilico.pl/modomics.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/aef87d005e8e3d58f0a0577a7be4d55a10c2d5b3
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
- Kevin V. Morris
- John S. Mattick
- Xiu-Jie Wang
- M. Manoharan
- Martin Egli
- Philipp Kapranov
- Marcel E. Dinger
- Howard Y. Chang
Citations in the corpus
- The rise of regulatory RNA (2014, background): “Moreover, apart from snoRNA-directed modifications, there are well over 100 other documented modifications of RNA 309,310 , including cytosine and adenosine methylation which have known physiological and cognitive effects 311–314 , indicating a new additional layer of RNA informational code and…”
- N6-methyl-adenosine (m6A) in RNA: An Old Modification with A Novel Epigenetic Function (2012, background): “More than 100 modifications have been identified in native cellular RNAs including mRNAs, tRNAs, rRNAs, small nuclear RNA (snRNAs) and small nucleolar RNAs (snoRNAs) [1,2].”
- Chemistry, structure and function of approved oligonucleotide therapeutics (2023, background): “More than 150 natural chemical modifications of RNA have been identified, among them 2′-O-methylation and complex decorations of nucleobases ((124) and cited refs.”