RNApathwaysDB - A database of RNA maturation and decay pathways

Nucleic Acids Research

Volumn 41, Issue D1, 2013, Pages

  Milanowska, Kaja ^a,b   Mikolajczak, Katarzyna ^b   Lukasik, Anna ^b   Skorupski, Marcin ^b   Balcer, Zuzanna ^b   Machnicka, Magdalena A ^a   Nowacka, Martyna ^a   Rother, Kristian M ^a,b   Bujnicki, Janusz M ^a,b  

^a INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

^b ADAM MICKIEWICZ UNIVERSITY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RIBOSOME RNA; TRANSFER RNA;

ARTICLE; COMPUTER MODEL; DATA ANALYSIS SOFTWARE; ESCHERICHIA COLI; HUMAN; INTERNET; NUCLEIC ACID DATABASE; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN RNA BINDING; RNA DECAY; RNA DEGRADATION; RNA MATURATION; RNA METABOLISM; RNA PROCESSING; SACCHAROMYCES CEREVISIAE;

DATABASES, NUCLEIC ACID; ENZYMES; ESCHERICHIA COLI; HUMANS; INTERNET; RNA; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA STABILITY; RNA, MESSENGER; RNA, RIBOSOMAL; RNA, TRANSFER; SACCHAROMYCES CEREVISIAE;

ESCHERICHIA COLI; HOMO SAPIENS; SACCHAROMYCES CEREVISIAE; SOLANUM TUBEROSUM;

EID: 84876527348     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1052     Document Type: Article

References (31)

1. Arraiano, C.M., Andrade, J.M., Domingues, S., Guinote, I.B., Malecki, M., Matos, R.G., Moreira, R.N., Pobre, V., Reis, F.P., Saramago, M. et al. (2010) The critical role of RNA processing and degradation in the control of gene expression. FEMS Microbiol. Rev., 34, 883-923.
2. Licatalosi, D.D. and Darnell, R.B. (2010) RNA processing and its regulation: global insights into biological networks. Nat. Rev. Genet., 11, 75-87.
3. Lutz, C.S. and Moreira, A. (2011) Alternative mRNA polyadenylation in eukaryotes: an effective regulator of gene expression. Wiley Interdiscip. Rev. RNA, 2, 22-31.
4. Motorin, Y. and Helm, M. (2011) RNA nucleotide methylation. Wiley Interdiscip. Rev. RNA, 2, 611-631.
5. Grosjean, H. (2005) Fine-Tuning of RNA Functions by Modification and Editing. Springer-Verlag, Berlin, Heidelberg.
6. Fatica, A. and Tollervey, D. (2002) Making ribosomes. Curr. Opin. Cell Biol., 14, 313-318.
7. Iglesias, N. and Stutz, F. (2008) Regulation of mRNP dynamics along the export pathway. FEBS Lett., 582, 1987-1996.
8. Holt, C.E. and Bullock, S.L. (2009) Subcellular mRNA localization in animal cells and why it matters. Science, 326, 1212-1216.
9. Hocine, S., Singer, R.H. and Grunwald, D. (2010) RNA processing and export. Cold Spring Harb. Perspect. Biol., 2, a000752.
10. Kushner, S.R. (2004) mRNA decay in prokaryotes and eukaryotes: different approaches to a similar problem. IUBMB Life, 56, 585-594.
11. Coller, J. and Parker, R. (2004) Eukaryotic mRNA decapping. Annu. Rev. Biochem., 73, 861-890.
12. Houseley, J. and Tollervey, D. (2009) The many pathways of RNA degradation. Cell, 136, 763-776.
13. Tomecki, R. and Dziembowski, A. (2010) Novel endoribonucleases as central players in various pathways of eukaryotic RNA metabolism. RNA, 16, 1692-1724.
14. Alonso, C.R. (2012) A complex 'mRNA degradation code' controls gene expression during animal development. Trends Genet., 28, 78-88.
15. Luna, R., Gaillard, H., Gonzalez-Aguilera, C. and Aguilera, A. (2008) Biogenesis of mRNPs: integrating different processes in the eukaryotic nucleus. Chromosoma, 117, 319-331.
16. Beggs, J.D. and Tollervey, D. (2005) Crosstalk between RNA metabolic pathways: an RNOMICS approach. Nat. Rev. Mol. Cell Biol., 6, 423-429.
17. Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. and Tanabe, M. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109-D114.
18. Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B. et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res., 39, D691-D697.
19. UniProt, C. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res., 40, D71-D75.
20. Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., Dicuccio, M., Federhen, S. et al. (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 40, D13-D25.
21. Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J. and Schomburg, D. (2011) BRENDA, the enzyme information system in 2011. Nucleic Acids Res., 39, D670-D676.
22. Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J. et al. (2012) The Pfam protein families database. Nucleic Acids Res., 40, D290-D301.
23. Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T.K., Bateman, A., Bernard, T., Binns, D., Bork, P., Burge, S. et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res., 40, D306-D312.
24. Gardner, P.P., Daub, J., Tate, J., Moore, B.L., Osuch, I.H., Griffiths-Jones, S., Finn, R.D., Nawrocki, E.P., Kolbe, D.L., Eddy, S.R. et al. (2011) Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res., 39, D141-D145.
25. Rose, P.W., Beran, B., Bi, C., Bluhm, W.F., Dimitropoulos, D., Goodsell, D.S., Prlic, A., Quesada, M., Quinn, G.B., Westbrook, J.D. et al. (2011) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res., 39, D392-D401.
26. Korneta, I., Magnus, M. and Bujnicki, J.M. (2012) Structural bioinformatics of the human spliceosomal proteome. Nucleic Acids Res., 40, 7046-7065.
27. Milanowska, K., Krwawicz, J., Papaj, G., Kosinski, J., Poleszak, K., Lesiak, J., Osinska, E., Rother, K. and Bujnicki, J.M. (2011) REPAIRtoire - a database of DNA repair pathways. Nucleic Acids Res., 39, D788-D792.
28. Caspi, R., Altman, T., Dreher, K., Fulcher, C.A., Subhraveti, P., Keseler, I.M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L.A. et al. (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res., 40, D742-D753.
29. Kelder, T., van Iersel, M.P., Hanspers, K., Kutmon, M., Conklin, B.R., Evelo, C.T. and Pico, A.R. (2012) WikiPathways: building research communities on biological pathways. Nucleic Acids Res., 40, D1301-D1307.
30. Czerwoniec, A., Dunin-Horkawicz, S., Purta, E., Kaminska, K.H., Kasprzak, J.M., Bujnicki, J.M., Grosjean, H. and Rother, K. (2009) MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res., 37, D118-D121.
31. Bateman, A., Agrawal, S., Birney, E., Bruford, E.A., Bujnicki, J.M., Cochrane, G., Cole, J.R., Dinger, M.E., Enright, A.J., Gardner, P.P. et al. (2011) RNAcentral: a vision for an international database of RNA sequences. RNA, 17, 1941-1946.