Biology:Nucleic acid modification databases

From HandWiki

This page compiles a list of databases, web portals and servers containing information on nucleic acid modification. RNA modification occurs in all living organisms, and is one of the most evolutionarily conserved properties of RNAs.[1][2][3] More than 100 different types of RNA modifications have been characterized across all living organisms. It can affect the activity, localization as well as stability of RNAs, and has been linked with human cancer and diseases.[1][2][3][4]

Name Scope Notes Type Link Ref
Molecules Cause of modification Data origin Addition Info?
RMBase mRNA, regulatory ncRNAs (e.g. lncRNAs, miRNAs) Natural high-throughput sequencing (pseudo-seq, Ψ-seq, CeU-seq, Aza-IP, MeRIP-seq, m6A-seq, miCLIP, m6A-CLIP, RiboMeth-seq) miRNA target sites, RNA-Binding Proteins (RBPs) Binding sites and disease-related SNPs database rna.sysu.edu.cn/rmbase/ [5]
MODOMICS Any RNA Natural and synthetic Curation modified ribonucleosides (symbols, chemical structures, biosynthetic pathways), RNA-modifying enzymes, location of modified residues in RNA sequences database modomics.genesilico.pl [6]
RNAmods Any RNA Natural ? modified ribonucleosides (symbols, chemical structures), distribution (type of molecule, phylogenetic domain) database rna.rega.kuleuven.be/rnamods [7]
DNAmod Any DNA Natural and synthetic Curation from ChEBI symbols, chemical structures database dnamod.hoffmanlab.org [8]
NAMDB DNA and RNA ? ? symbols, chemical structures; for some entries: location and frequency, enzymes and reactions database www.namdb.cn/index.php

References

  1. ↑ 1.0 1.1 Li, S; Mason, CE (2013). "The pivotal regulatory landscape of RNA modifications.". Annual Review of Genomics and Human Genetics 15: 127–50. doi:10.1146/annurev-genom-090413-025405. PMID 24898039. 
  2. ↑ 2.0 2.1 Song, CX; Yi, C; He, C (October 2012). "Mapping recently identified nucleotide variants in the genome and transcriptome.". Nature Biotechnology 30 (11): 1107–16. doi:10.1038/nbt.2398. PMID 23138310. 
  3. ↑ 3.0 3.1 Meyer, KD; Jaffrey, SR (April 2014). "The dynamic epitranscriptome: N6-methyladenosine and gene expression control.". Nature Reviews Molecular Cell Biology 15 (5): 313–26. doi:10.1038/nrm3785. PMID 24713629. 
  4. ↑ Jonkhout, Nicky; Tran, Julia; Smith, Martin Alexander; Schonrock, Nicole; Mattick, John S; Novoa, Eva Maria (30 August 2017). "The RNA modification landscape in human disease". RNA 23 (12): 1754–1769. doi:10.1261/rna.063503.117. PMID 28855326. 
  5. ↑ Sun, WJ; Li, JH; Liu, S; Wu, J; Zhou, H; Qu, LH; Yang, JH (11 October 2015). "RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data.". Nucleic Acids Research 44 (D1): D259–D265. doi:10.1093/nar/gkv1036. PMID 26464443. 
  6. ↑ Machnicka, MA; Milanowska, K; Osman Oglou, O; Purta, E; Kurkowska, M; Olchowik, A; Januszewski, W; Kalinowski, S et al. (December 2012). "MODOMICS: a database of RNA modification pathways--2013 update.". Nucleic Acids Research 41 (Database issue): D262-7. doi:10.1093/nar/gks1007. PMID 23118484. 
  7. ↑ Cantara, WA; Crain, PF; Rozenski, J; McCloskey, JA; Harris, KA; Zhang, X; Vendeix, FA; Fabris, D et al. (December 2010). "The RNA Modification Database, RNAMDB: 2011 update.". Nucleic Acids Research 39 (Database issue): D195-201. doi:10.1093/nar/gkq1028. PMID 21071406. 
  8. ↑ Sood, Ankur Jai; Viner, Coby; Hoffman, Michael M. (December 2019). "DNAmod: the DNA modification database". Journal of Cheminformatics 11 (1): 30. doi:10.1186/s13321-019-0349-4. PMID 31016417. 



Retrieved from "https://handwiki.org/wiki/index.php?title=Biology:Nucleic_acid_modification_databases&oldid=4063526"