Detecting transcriptionally active regions using genomic tiling arrays

Genome Biology

Volumn 7, Issue 7, 2006, Pages

  Halasz, Gabor ^a   van Batenburg, Marinus F ^a,b   Perusse, Joelle ^c   Hua, Sujun ^c   Lu, Xiang Jun ^a   White, Kevin P ^c,d   Bussemaker, Harmen J ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

^c YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANOPHELES GAMBIAE; ARTICLE; COMPUTER PROGRAM; DATA ANALYSIS; DNA MICROARRAY; GENE LOCUS; GENETIC TRANSCRIPTION; GENOMICS; HUMAN CHROMOSOME; NONHUMAN; ANIMAL; GENETICS; HUMAN; NUCLEIC ACID HYBRIDIZATION; SENSITIVITY AND SPECIFICITY;

ANOPHELES GAMBIAE;

ANIMALS; ANOPHELES GAMBIAE; CHROMOSOMES, HUMAN; GENOMICS; HUMANS; NUCLEIC ACID HYBRIDIZATION; SENSITIVITY AND SPECIFICITY; TRANSCRIPTION, GENETIC;

EID: 33750492614     PISSN: 1474760X     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2006-7-7-r59     Document Type: Article

References (35)

1. Hogenesch JB, Ching KA, Batalov S, Su AI, Walker JR, Zhou Y, Kay SA, Schultz PG, Cooke MP: A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell 2001, 106:413-415.
2. Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, et al.: Global identification of human transcribed sequences with genome tiling arrays. Science 2004, 306:2242-2246.
3. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, et al.: Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 2005, 308:1149-1154.
4. David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bolkin L, Jones T, Davis RW, Steinmetz LM: A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci USA 2006, 103:5320-5325.
5. Frey BJ, Mohammad N, Morris QD, Zhang W, Robinson MD, Mnaimneh S, Chang R, Pan Q, Sat E, Rossant J, et al: Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs. Nat Genet 2005, 37:991-996.
6. Kampa D, Cheng, J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, Drenkow J, Piccolboni A, Bekiranov S, Helt G, et al.: Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res 2004, 14:331-342.
7. Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, Gingeras TR: Large-scale transcriptional activity in chromosomes 21 and 22. Science 2002, 296:916-919.
8. Li L, Wang X, Stolc V, Li X, Zhang D, Su N, Tongprasit W, Li S, Cheng Z, Wang J, Deng XW: Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 2006, 38:124-129.
9. Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, et al.: The transcriptional activity of human Chromosome 22. Genes Dev 2003, 17:529-540.
10. Samanta MP, Tongprasit W, Sethi H, Chin CS, Stolc V: Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway. Proc Natl Acad Sci USA 2006, 103:4192-4197.
11. Schadt EE, Edwards SW, Guha Thakurta D, Holder D, Ying LVS, Svetnik V, Hart KW, Russell A, Li G, Cavet C, et al: A comprehensive transcript index of the human genome generated using microarrays and computational approaches. Genome Biol 2004, 5:R73.
12. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU: A gene expression map of Arabidopsis thaliana development. Nat Genet 2005, 37:501-506.
13. Stolc V, Gauhar Z, Mason C, Halasz G, van Batenburg MF, Rifkin SA, Hua S, Herreman, T, Tongprasit W, Barbano PE, et al.: A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 2004, 306:655-660.
14. Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, et al.: Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 2003, 302:842-846.
15. Shoemaker DD, Schadt EE, Armour CD, He YD, Garrett-Engele P, McDonagh PD, Loerch PM, Leonardson A, Lum PY, Cavet G, et al.: Experimental annotation of the human genome using microarray technology. Nature 2001, 409:922-927.
16. Royce TE, Rozowsky JS, Bertone P, Samanta M, Stolc V, Weissman S, Snyder M, Gerstein M: Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet 2005, 21:466-475.
17. Frey BJ, Morris QD, Zhang W, Mohammad N, Hughes TR: Genrate: a generative model that finds and scores new genes and exons in genomic microarray data. Pac Symp Biocomput 2005:495-506.
18. Hubbell E, Liu WM, Mei R: Robust estimators for expression analysis. Bioinformatics 2002, 18:1585-1592.
19. Li C, Wong WH: Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 2001, 98:31-36.
20. Kerr MK, Churchill GA: Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments. Proc Natl Acad Sci USA 2001, 98:8961-8965.
21. Hekstra D, Taussig AR, Magnasco M, Naef F: Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays. Nucleic Acids Res 2003, 31:1962-1968.
22. Held GA, Grinstein G, Tu Y: Modeling of DNA microarray data by using physical properties of hybridization. Proc Natl Acad Sci USA 2003, 100:7575-7580.
23. Mei R, Hubbell E, Bekiranov S, Mittmann M, Christians FC, Shen MM, Lu G, Fang J, Liu WM, Ryder T, et al.: Probe selection for high-density oligonucleotide arrays. Proc Natl Acad Sci USA 2003, 100:11237-11242.
24. Zhang L, Miles MF, Aldape KD: A model of molecular interactions on short oligonucleotide microarrays [see comment]. Nature Biotechnol 2003, 21:818-821.
25. Wu Z, Irizarry RA, Gentleman R, Murillo FM, Spencer F: A Model Based Background Adjustment for Oligonucleotide Expression Arrays. In Department of Biostatistics Working Papers Baltimore, MD: John Hopkins University: 2004.
26. Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high dnsity oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193.
27. Naef F, Magnasco MO: Solving the riddle of the bright mis-matches: labelling and effective binding in oligonucleotide arrays. Phys Rev E Stat Nonlin Soft Matter Phys 2003, 68:011906.
28. Fisher RA: Statistical Methods for Research Workers 11th edition. Edinburgh: Oliver & Boyd; 1950.
29. Bailey TL, Gribskov M: Estimating and evaluating the statistics of gapped local-alignment scores. J Comput Biol 2002, 9:575-593.
30. Huang JC, Morris QD, Hughes TR, Frey BJ: GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data. Bioinformatics 2005, 21(Suppl 1):i222-i231.
31. Transcription Detector Information and Software [http://bussemakerlab.org/software/TranscriptionDetector/]
32. Nuwaysir EF, Huang W, Albert TJ, Singh J, Nuwaysir K, Pitas A, Richmond T, Gorski T, Berg JP, Bailin J, et al.: Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res 2002, 12:1749-1755.
33. Benjamini YH, Yosef: Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc 1995, 57:289-300.
34. Affymetrix Human Transcriptome Project. [http://transcriptome. affymetrix.com/publication/transcriptome_10chromosomes/]
35. UCSC Genome Annotation Database [http://hgdownload.cse.ucsc.edu/ goldenpath/10april2003/database/]