MODOMICS: a database of RNA modification pathways
By Stanislaw Dunin-Horkawicz, Anna Czerwoniec, Michal J. Gajda, M. Feder, Henri Grosjean, Janusz M. Bujnicki. Nucleic Acids Res., 2005
1,188 citations recorded by the source corpus.
MODOMICS is the first comprehensive database resource for systems biology of RNA modification. It integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that carry out the respective reactions. MODOMICS also provides literature information, and links to other databases, including the available protein sequence and structure data. The current list of modifications and pathways is comprehensive, while the dataset of enzymes is limited to Escherichia coli and Saccharomyces cerevisiae and sequence alignments are presented only for tRNAs from these organisms. RNAs and enzymes from other organisms will be included in the near future. MODOMICS can be queried by the type of nucleoside (e.g. A, G, C, U, I, m1A, nm5s2U, etc.), type of RNA, position of a particular nucleoside, type of reaction (e.g. methylation, thiolation, deamination, etc.) and name or sequence of an enzyme of interest. Options for data presentation include graphs of pathways involving the query nucleoside, multiple sequence alignments of RNA sequences and tabular forms with enzyme and literature data. The contents of MODOMICS can be accessed through the World Wide Web at .
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/5745c2aff2a61d6f4a5b1083663fe7ed54d22672
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Citations in the corpus
- MODOMICS: a database of RNA modification pathways—2013 update (2012, background): “More than one hundred functionally and structurally characterized proteins have been added since the previous release (31) and the collection of protein sequences has been updated accordingly.”
- ModeRNA: a tool for comparative modeling of RNA 3D structure (2011, methodology): “To date, 115 different nucleotide modifications have been characterized, and this number is still growing (36).”
- Where, when and how: context-dependent functions of RNA methylation writers, readers, and erasers (2019, background): “More than 150 distinct chemical marks on cellular RNA have been identified to date (Boccaletto et al., 2018) since the discovery the first structurally modified nucleoside, pseudo-uridine, in the 1950s (Cohn and Volkin, 1951).”
- m6A regulator-mediated methylation modification patterns and tumor microenvironment infiltration characterization in gastric cancer (2020, background): “more than 150 RNA modifications including 5methylcytosine (m(5)C), N6-methyladenosine (m(6)A) and N1-methyladenosine (m(1)A) have been identified [1, 2].”
- Targeting FTO suppresses cancer stem cell maintenance and immune evasion (2020, positive): “A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript INTRODUCTION Among the >170 modified RNA nucleotides, N6-methyladenosine (m6A) represents the most abundant and prevalent internal modification in eukaryotic mRNA (Boccaletto et al., 2018; Frye et al., 2018).”
- BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA (2012, neutral): “In this respect it is different from other enzyme databases which are specialized either on the nomenclature [ExplorEnz, ENZYME (20), IntEnz (21)], on the metabolic pathways (e.g. KEGG, MetaCyc) or on specific classes of enzymes [e.g. Merops (22), MODOMICS (23), CAZy (24), Kinomer (25)].”
- Focused classification and refinement in high-resolution cryo-EM structural analysis of ribosome complexes. (2017, background): “More than 140 chemical modifications are reported based on biophysical and biochemical studies [73].”