TileProbe: Modeling tiling array probe effects using publicly available data

Bioinformatics

Volumn 25, Issue 18, 2009, Pages 2369-2375

  Judy, Jennifer Toolan ^a   Ji, Hongkai ^a  

^a JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESTROGEN RECEPTOR; MYC PROTEIN; TRANSCRIPTION FACTOR GLI3;

ALGORITHM; ARTICLE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DATA BASE; DNA BINDING MOTIF; GENE EXPRESSION PROFILING; HIGH THROUGHPUT SCREENING; INFORMATION PROCESSING; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; PRIORITY JOURNAL;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 69849089440     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp425     Document Type: Article

References (26)

1. Barrett,T. et al. (2007) NCBI GEO: Mining tens of millions of ex-pression profiles - database and tools update. Nucleic Acids Res. 35, D760-D765.
2. Bernstein,B.E. et al. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell, 125, 315-326.
3. Bertone,P. et al. (2004) Global identification of human transcribed sequences with genome tiling arrays. Science, 306 2242-2246.
4. Bolstad,B.M. et al. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193.
5. Carroll,J.S. et al. (2005) Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell, 122, 33-43.
6. Cawley,S. et al. (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell, 116, 499-509.
7. Huber,W. et al. (2006) Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics, 22, 1963-1970.
8. Irizarry,R.A. et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249-264.
9. Ji,H. and Wong,W.H. (2005) TileMap: Create chromosomal map of tiling array hybridizations. Bioinformatics, 21, 3629-3636.
10. Ji,H. et al. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol., 26, 1293-1300.
11. Johnson,W.E. et al. (2006) Model-based analysis of tiling-arrays for ChIP-chip. Proc. Natl. Acad. Sci. USA, 103, 12457-12462.
12. Kampa,D. et al. (2004) Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res., 14, 331-342.
13. Kapranov,P. et al. (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science, 296, 916-919.
14. Kapur,K. et al. (2007) Exon array assessment of gene expression. Genome Biol., 8, R82.
15. Keles,S. et al. (2006) Multiple testing methods for ChIP-Chip high density oligonucleotide array data. J. Comput. Biol., 13, 579-613.
16. Li,C. and Wong,W.H. (2001) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc. Natl Acad. Sci. USA, 98, 31-36.
17. Li,W. et al. (2005) A hidden markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics, 21(Suppl 1), i274-i282.
18. Liu,X.S. (2007) Getting started in tiling microarray analysis. PLoS Comput. Biol., 3, e183.
19. Ozsolak,F. et al. (2007) High-throughput mapping of the chromatin structure of human promoters. Nat. Biotechnol., 25, 244-248.
20. Shendure,J. and Ji,H. (2008) Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135-1145.
21. Urban,A.E. et al. (2006) High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc. Natl Acad. Sci. USA, 103, 4534-4539.
22. Weber,M. et al. (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet., 39, 457-466.
23. Wu,Z. et al. (2004) A model based background adjustement for oligonucleotide expression arrays. J. Am. Stat. Assoc., 99, 909-917.
24. Yuan,G.C. et al. (2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science, 309, 626-630.
25. Zhang,X. et al. (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell, 126, 1189-1201.
26. Zilliox,M.J. and Irizarry,R.A. (2007) A gene expression bar code for microarray data. Nat. Methods, 4, 911-913.