HALO-a Java framework for precise transcript half-life determination

Bioinformatics

Volumn 26, Issue 9, 2010, Pages 1264-1266

  Friedel, Caroline C ^a   Kaufmann, Stefanie ^a   Dölken, Lars ^b   Zimmer, Ralf ^a  

^a Institut für Informatik   (Germany)

^b UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RNA;

ALGORITHM; ARTICLE; BIOLOGY; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER LANGUAGE; COMPUTER PROGRAM; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENOME; METABOLISM; METHODOLOGY; RNA STABILITY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; GENE EXPRESSION PROFILING; GENOME; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGRAMMING LANGUAGES; RNA; RNA STABILITY; RNA, MESSENGER; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 77952850620     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq117     Document Type: Article

References (21)

1. Bernstein, J.A. et al. (2002) Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc. Natl Acad. Sci. USA, 99, 9697-9702.
2. Blattner, C. et al. (2000) UV-Induced stabilization of c-fos and other short-lived mRNAs. Mol. Cell Biol., 20, 3616-3625.
3. Cleary, M.D. et al. (2005) Biosynthetic labeling of RNA with uracil phosphori-bosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay. Nat. Biotechnol., 23, 232-237.
4. Dölken, L. et al. (2008) High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA, 14, 1959-1972.
5. Fan, J. et al. (2002) Global analysis of stress-regulated mRNA turnover by using cDNA arrays. Proc. Natl Acad. Sci. USA, 99, 10611-10616.
6. Friedel, C.C. and Dölken, L. (2009) Metabolic tagging and purification of nascent RNA: implications for transcriptomics. Mol. Biosyst., 5, 1271-1278.
7. Friedel, C.C. et al. (2009) Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res., 37, e115.
8. García-Martínez, J. et al. (2004) Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol. Cell, 15, 303-313.
9. Gorospe, M. et al. (1998) p53-dependent elevation of p21Waf1 expression by UVlight is mediated through mRNA stabilization and involves a vanadate-sensitive regulatory system. Mol. Cell Biol., 18, 1400-1407.
10. Kenzelmann, M. et al. (2007) Microarray analysis of newly synthesized RNA in cells and animals. Proc. Natl Acad. Sci. USA, 104, 6164-6169.
11. Mann, M. (2006) Functional and quantitative proteomics using SILAC. Nat. Rev. Mol. Cell Biol., 7, 952-958.
12. Miller, M.R. et al. (2009) TU-tagging: cell type-specific RNA isolation from intact complex tissues. Nat. Methods, 6, 439-441.
13. Molina-Navarro, M.M. et al. (2008) Comprehensive transcriptional analysis of the oxidative response in yeast. J. Biol. Chem., 283, 17908-17918.
14. Narsai, R. et al. (2007) Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana. Plant Cell, 19, 3418-3436.
15. Ong, S.-E. et al. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics, 1, 376-386.
16. Raghavan, A. et al. (2002) Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes. Nucleic Acids Res., 30, 5529-5538.
17. Redon, E. et al. (2005) Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J. Biol. Chem., 280, 36380-36385.
18. Ross, J. (1995) mRNA stability in mammalian cells. Microbiol. Rev., 59, 423-450.
19. Wang, Y. et al. (2002) Precision and functional specificity in mRNA decay. Proc. Natl Acad. Sci. USA, 99, 5860-5865.
20. Wu, Z. and Irizarry, R.A. (2004) Preprocessing of oligonucleotide array data. Nat. Biotechnol., 22, 656-658.
21. Yang, E. et al. (2003) Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome Res., 13, 1863-1872.