[14] Microarray Analysis of RNA Processing and Modification

Methods in Enzymology

Volumn 410, Issue , 2006, Pages 300-316

  Hughes, Timothy R ^a   Hiley, Shawna L ^a   Saltzman, Arneet L ^a   Babak, Tomas ^a   Blencowe, Benjamin J ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

CONTROLLED STUDY; NONHUMAN; NORTHERN BLOTTING; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; RNA ANALYSIS; RNA PROCESSING; RNA SEQUENCE; RNA SPLICING; SACCHAROMYCES CEREVISIAE; ANIMAL; DNA MICROARRAY; HUMAN; METABOLISM; METHODOLOGY; SEQUENCE ANALYSIS;

ANIMALS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA; RNA PROCESSING, POST-TRANSCRIPTIONAL; SEQUENCE ANALYSIS, RNA;

EID: 33747814806     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(06)10014-2     Document Type: Review

References (27)

1. Babak T., Zhang W., Morris Q., Blencowe B.J., and Hughes T.R. Probing microRNAs with microarrays: Tissue specificity and functional inference. RNA 10 (2004) 1813-1819
2. Blanchette M., Green R.E., Brenner S.E., and Rio D.C. Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. Genes Dev. 19 (2005) 1306-1314
3. Boorstein W.R., and Craig E.A. Primer extension analysis of RNA. In: Dahlberg J., and Abelson J. (Eds). "RNA Processing Part A, General Methods" Vol. 180 (1989), Elsevier Science & Technology Books 262-288
4. Breslauer K.J., Frank R., Blocker H., and Marky L.A. Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA 83 (1986) 3746-3750
5. Clark T.A., Sugnet C.W., and Ares Jr. M. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296 (2002) 907-910
6. Fehlbaum P., Guihal C., Bracco L., and Cochet O. A microarray configuration to quantify expression levels and relative abundance of splice variants. Nucleic Acids Res. 33 (2005) e47
7. Gentleman R.C., Carey V.J., Bates D.M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li C., Maechler M., Rossini A.J., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J.Y., and Zhang J. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 5 (2004) R80
8. Hegde P., Qi R., Abernathy K., Gay C., Dharap S., Gaspard R., Hughes J.E., Snesrud E., Lee N., and Quackenbush J. A concise guide to cDNA microarray analysis. Biotechniques 29 (2000) 548-550 552-554, 556 passim.
9. Hiley S.L., Babak T., and Hughes T.R. Global analysis of yeast RNA processing identifies new targets of RNase III and uncovers a link between tRNA 5′ end processing and tRNA splicing. Nucleic Acids Res. 33 (2005) 3048-3056
10. Hiley S.L., Jackman J., Babak T., Trochesset M., Morris Q.D., Phizicky E., and Hughes T.R. Detection and discovery of RNA modifications using microarrays. Nucleic Acids Res. 33 (2005) e2
11. Huber W., von Heydebreck A., Sultmann H., Poustka A., and Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18 Suppl .1 (2002) S96-S104
12. Hughes T.R., Mao M., Jones A.R., Burchard J., Marton M.J., Shannon K.W., Lefkowitz S.M., Ziman M., Schelter J.M., Meyer M.R., Kobayashi S., Davis C., Dai H., He Y.D., Stephaniants S.B., Cavet G., Walker W.L., West A., Coffey E., Shoemaker D.D., Stoughton R., Blanchard A.P., Friend S.H., and Linsley P.S. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19 (2001) 342-347
13. Inada M., and Guthrie C. Identification of Lhp1p-associated RNAs by microarray analysis in Saccharomyces cerevisiae reveals association with coding and noncoding RNAs. Proc. Natl. Acad. Sci. USA 101 (2004) 434-439
14. Johnson J.M., Castle J., Garrett-Engele P., Kan Z., Loerch P.M., Armour C.D., Santos R., Schadt E.E., Stoughton R., and Shoemaker D.D. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302 (2003) 2141-2144
15. Le K., Mitsouras K., Roy M., Wang Q., Xu Q., Nelson S.F., and Lee C. Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. Nucleic Acids Res. 32 (2004) e180
16. Pan Q., Bakowski M.A., Morris Q., Zhang W., Frey B.J., Hughes T.R., and Blencowe B.J. Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet. 21 (2005) 73-77
17. Pan Q., Shai O., Misquitta C., Zhang W., Saltzman A.L., Mohammad N., Babak T., Siu H., Hughes T.R., Morris Q.D., Frey B.J., and Blencowe B.J. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol. Cell 16 (2004) 929-941
18. Peng W.T., Robinson M.D., Mnaimneh S., Krogan N.J., Cagney G., Morris Q., Davierwala A.P., Grigull J., Yang X., Zhang W., Mitsakakis N., Ryan O.W., Datta N., Jojic V., Pal C., Canadien V., Richards D., Beattie B., Wu L.F., Altschuler S.J., Roweis S., Frey B.J., Emili A., Greenblatt J.F., and Hughes T.R. A panoramic view of yeast noncoding RNA processing. Cell 113 (2003) 919-933
19. Shai O., Morris Q.D., Blencowe B.J., and Frey B.J. Inferring global levels of alternative splicing isoforms using a generative model of microarray date. Bioinformatics 22 (2006) 606-613
20. Shoemaker D.D., Schadt E.E., Armour C.D., He Y.D., Garrett-Engele P., McDonagh P.D., Loerch P.M., Leonardson A., Lum P.Y., Cavet G., Wu L.F., Altschuler S.J., Edwards S., King J., Tsang J.S., Schimmack G., Schelter J.M., Koch J., Ziman M., Marton M.J., Li B., Cundiff P., Ward T., Castle J., Krolewski M., Meyer M.R., Mao M., Burchard J., Kidd M.J., Dai H., Phillips J.W., Linsley P.S., Stoughton R., Scherer S., and Boguski M.S. Experimental annotation of the human genome using microarray technology. Nature 409 (2001) 922-927
21. Sugimoto N., Nakano S., Yoneyama M., and Honda K. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res. 24 (1996) 4501-4505
22. Wang H., Hubbell E., Hu J.S., Mei G., Cline M., Lu G., Clark T., Siani-Rose M.A., Ares M., Kulp D.C., and Haussler D. Gene structure-based splice variant deconvolution using a microarray platform. Bioinformatics 19 Suppl. 1 (2003) i315-i322
23. Wiegant J.C., van Gijlswijk R.P., Heetebrij R.J., Bezrookove V., Raap A.K., and Tanke H.J. ULS: A versatile method of labeling nucleic acids for FISH based on a monofunctional reaction of cisplatin derivatives with guanine moieties. Cytogenet. Cell Genet. 87 (1999) 47-52
24. Wolber P.K., Collins P.J., Lucas A.B., De Witte A., and Shannon K.W. The Agilent in situ-synthesized microarray platform. Methods Enzymol. 410 this volume (2006) 28-57
25. Xing F., Hiley S.L., Hughes T.R., and Phizicky E.M. The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs. J. Biol. Chem. 279 (2004) 17850-17860
26. Yang Y.H., Dudoit S., Luu P., Lin D.M., Peng V., Ngai J., and Speed T.P. Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30 (2002) e15
27. Yeakley J.M., Fan J.B., Doucet D., Luo L., Wickham E., Ye Z., Chee M.S., and Fu X.D. Profiling alternative splicing on fiber-optic arrays. Nat. Biotechnol. 20 (2002) 353-358