Differential analysis for high density tiling microarray data

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Ghosh, Srinka ^a   Hirsch, Heather A ^b   Sekinger, Edward A ^c   Kapranov, Philipp ^a   Struhl, Kevin ^b   Gingeras, Thomas R ^a  

^a Thermo Fisher Scientific   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c ASURAGEN INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONSISTENT SAMPLINGS; DIFFERENTIAL ANALYSIS; DIFFERENTIAL EXPRESSIONS; DIFFERENTIAL RESPONSE; OLIGONUCLEOTIDE TILING ARRAYS; SIGNIFICANCE ANALYSIS OF MICROARRAYS; TIME-COURSE EXPERIMENTS; TRANSCRIPTION FACTOR BINDING;

MICROARRAYS; OLIGONUCLEOTIDES; TRANSCRIPTION;

GENES;

DNA; RNA; RETINOIC ACID;

AB INITIO CALCULATION; ALGORITHM; ANALYTIC METHOD; ARTICLE; BIOINFORMATICS; CHROMATIN STRUCTURE; DNA MICROARRAY; EXON; GENE CONTROL; GENE EXPRESSION; GENOME; GENOME ANALYSIS; INTRON; MICROARRAY ANALYSIS; RNA TRANSCRIPTION; TRANSCRIPTION REGULATION; BIOLOGICAL MODEL; BIOLOGY; CELL STRAIN HL 60; CHEMISTRY; CHROMOSOME MAP; DECISION THEORY; DNA PROBE; DRUG EFFECT; GENE EXPRESSION PROFILING; GENE STRUCTURE; GENETIC TRANSCRIPTION; GENETICS; GENOMICS; HUMAN; METHODOLOGY; PHYSIOLOGY; PREDICTION AND FORECASTING; REGULATORY SEQUENCE;

TETRA;

ALGORITHMS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DECISION THEORY; DNA PROBES; GENE COMPONENTS; GENE EXPRESSION PROFILING; GENOMICS; HL-60 CELLS; HUMANS; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PREDICTIVE VALUE OF TESTS; REGULATORY SEQUENCES, NUCLEIC ACID; TRANSCRIPTION, GENETIC; TRETINOIN;

EID: 38949141635     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-359     Document Type: Article

References (55)

1. Elvidge G Microarray expression technology: From start to finish Pharmacogenomics 2006, 7:123-34. 10.2217/14622416.7.1.123 16354130
2. Zhang X Kluger Y Nakayama Y Poddar R Whitney C Detora A Weissman SM Newburger PE Gene expression in mature neutrophils: Early responses to inflammatory stimuli. Journal of leukocyte biology Journal Leukoc Biol 2004, 75(2):358-72. 10.1189/jlb.0903412
3. Werner SL Barken D Hoffmann A Stimulus Specificity of Gene Expression Programs Determined by Temporal Control of IKK Activity Science 2005, 309(5742):1857-61. 10.1126/science.1113319 16166517
4. Grigoryev DN Ma SF Irizarry RA Ye SQ Quackenbush J Garcia JGN Orthologous gene-expression profiling in multi-species models search for candidate genes Genome Biology 2004, 5:R34. 416470 15128448 10.1186/ gb-2004-5-5-r34
5. Tusher VG Tibshirani R Chu G Significance analysis of microarrays applied to the ionizing radiation response PNAS 2001, 98(9):5116-21. 33173 11309499 10.1073/pnas.091062498
6. Strimmer K Modeling gene expression measurement error: A quasi-likelihood approach BMC BioInformatics 2003, 4:10. 153502 12659637 10.1186/1471-2105-4-10
7. Benjamini Y Hochberg Y Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing Journal of the Royal Statistical Society B 1995, 57:289-300.
8. Dudoit S van der Laan MJ Pollard KS Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates Statistical Applications in Genetics and Molecular Biology 2004, 3(1):ARticle 13. 10.2202/1544-6115.1040
9. van der Laan MJ Dudoit S Pollard KS Multiple testing. Part II. Step-down procedures for control of the family-wise error rate Statistical Applications in Genetics and Molecular Biology 2004, 3(1):ARticle 14.
10. Pounds SB Estimation and control of multiple testing error rates for microarray studies Briefings in Bioinformatics 2006, 7(1):25-36. 10.1093/ bib/bbk002 16761362
11. Dudoit S Yang YH Callow MJ Speed TP Statistical Methods for Identifying Differentially Expressed Genes in Replicated cDNA Microarray Experiments Technical Report # 578 2000.
12. Benjamini Y Hochberg Y On the Adaptive Control of the False Discovery Rate in Multiple Testing with Independent Statistics Journal of Educational and Behavioral Statistics 2000, 25(1):60-83.
13. Holm S A Simple Sequentially Rejective Bonferroni Test Procedure Scandinavian Journal of Statistics 1979, 6:65-70.
14. Westfall PH Young SS Resampling-based Multiple Testing Wiley, New York 1993.
15. Benjamini Y Yekutieli D The Control of the False Discovery Rate in Multiple Testing under Dependency The Annals of Statistics 2001, 29:1165-88. 10.1214/aos/1013699998
16. Yekutieli D Benjamini Y Resampling-based False Discovery Rate Controlling Multiple Test Procedures for Correlated Test Statistics Journal of Statistical Planning and Inference 1999, 82:171-196. 10.1016/ S0378-3758(99)00041-5
17. Efron B Tibshirani R Storey JD Tusher V Empirical Bayes Analysis of a Microarray Experiment Journal of the American Statistical Association 2001, 96:1151-60. 10.1198/016214501753382129
18. Storey JD A Direct Approach to False Discovery Rates Journal of the Royal Statistical Society, Series B 2002, 64:479-98. 10.1111/ 1467-9868.00346
19. Storey JD Taylor JE Siegmund D Strong Control, Conservative Point Estimation, and Simultaneous Conservative Consistency of False Discovery Rates: A Unified Approach Journal of the Royal Statistical Society, Series B 2004, 66:187-205. 10.1111/j.1467-9868.2004.00439.x
20. The ENCODE Project Consortium The ENCODE Project Science 2004, 306:636-40. 10.1126/science.1105136 15499007
21. The ENCODE datasets can be downloaded from the following website http://genome.ucsc.edu/ENCODE/encode.hg17.html
22. The ENCODE Project Consortium The ENCODE pilot project: Identification and analysis of functional elements in 1 percent of the human genome Nature 2007, 447:799-816. 10.1038/nature05874 17571346
23. Kapranov P Cawley SE Drenkow J Bekiranov S Strausberg RL Fodor SPA Gingeras TR Large Scale Transcriptional Activity in Chromosomes 21 and 22 Science 2002, 296:916-9. 10.1126/science.1068597 11988577
24. Cheng J Kapranov P Drenkow J Dike S Brubaker S Patel S Long J Stern D Tammana H Helt G Sementchenko V Piccolboni A Bekiranov S Bailey DK Ganesh M Ghosh S Bell I Gerhard DS Gingeras TR Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution Science 2005, 307:. 15731445
25. Kampa D Cheng J Kapranov P Yamanaka M Brubaker S Cawley SE Drenkow J Piccolboni A Bekiranov S Helt G Tammana H Gingeras TR Novel RNAs Identified from an In-depth Analysis of the Transcriptome of Human Chromosomes 21 and 22 Genome Research 2004, 14(3):331-42. 353210 14993201 10.1101/gr.2094104
26. Ren B Robert F Wyrick JJ Aparicio O Jennings EG Simon I Zeitlinger J Schreiber J Hannett N Kanin E Volkert TL Wilson CJ Bell SP Young RA Genome-wide location and function of DNA binding proteins Science 2000, 290:2306-9. 10.1126/science.290.5500.2306 11125145
27. Iyer VR Horak CE Scafe CS Botstein D Snyder M Brown PO Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF Nature 2001, 409(6819):533-8. 10.1038/35054095 11206552
28. Horak CE Snyder M ChIP-chip: A genomic approach for identifying transcription factor binding sites Methods in Enzymology 2002, 350:469-83. 12073330
29. Oberley MJ Tsao J Yau P Farnham PJ High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays Methods in Enzymology 2004, 376:315-33. 14975315
30. Weinmann AS Yan PS Oberley MJ Huang H-MT Farnham PJ Isolating human transcription factor targets by combining chromatin immunoprecipitation and CpG microarray analysis Genes & Devel 2002, 16:235-44. 10.1101/ gad.943102
31. Cawley SE Bekiranov S Ng HH Kapranov P Sekinger EA Kampa D Piccolboni A Sementchenko V Cheng J Williams AJ Wheeler R Wong B Drenkow J Yamanaka M Patel S Brubaker S Tammana H Helt G Struhl K Gingeras TR Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs Cell 2004, 116:499-509. 10.1016/S0092-8674(04)00127-8 14980218
32. Lieb JD Liu X Botstein D Brown PO Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association Nat Genet 2001, 28:327-34. 10.1038/ng569 11455386
33. Buck MJ Lieb JD ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments Genomics 2004, 83:349-60. 10.1016/j.ygeno.2003.11.004 14986705
34. Yang A Zhu Z Kapranov P McKeon F Church GM Gingeras TR Struhl K Relationships between p63 Binding, DNA Sequence, Transcription Activity, and Biological Function in Human Cells Molecular Cell 2006, 24:593-602. 10.1016/j.molcel.2006.10.018 17188034
35. Fodor SP Read JL Pirrung MC Stryer L Lu AT Solas D Light directed spatially addressable parallel chemical synthesis Science 1991, 251:767-73. 10.1126/science.1990438 1990438
36. Fodor SP Rava RP Huang XC Pease AC Holmes CP Adams CL Multiplexed biochemical assays with biological chips Nature 1993, 364:555-6. 10.1038/ 364555a0 7687751
37. Lipshutz R Fodor SP Gingeras TR Lockhart D High density synthetic oligonucleotide arrays Nat Genet 1999, 21(1 Suppl):20-4. 10.1038/4447 9915496
38. Kapranov P Sementchenko VI Gingeras TR Beyond expression profiling: Next generation uses of high density oligonucleotide arrays Brief Funct Genomic Proteomic 2003, 2:47-56. 10.1093/bfgp/2.1.47 15239943
39. Mockler TC Ecker JR Applications of DNA tiling arrays for whole-genome analysis Genomics 2005, 85:1-15. 10.1016/j.ygeno.2004.10.005 15607417
40. Bertone P Gerstein M Synder M Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery Chromosome Research 2005, 13:259-74. 10.1007/s10577-005-2165-0 15868420
41. Bolstad B Probe Level Quantile Normalization of high Density Oligonucleotide Array Data http://bmbolstad.com/stuff/qnorm.pdf
42. Bolstad B Irizarry R Astrand M Speed T Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance Bioinformatics 2003, 19:185-93. 10.1093/bioinformatics/19.2.185 12538238
43. Ghosh S Hirsch H Sekinger E Struhl K Gingeras T Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments BMC Bioinformatics 2006, 7:434. 1615882 17022824 10.1186/1471-2105-7-434
44. Martone R Euskirchen G Bertone P Hartman S Royce TE Luscombe NM Rinn JL Nelson FK Miller P Gerstein M Weissman S Snyder M Distribution of NF-kappaB-binding sites across human chromosome 22 PNAS 2003, 100:12247-52. 218744 14527995 10.1073/pnas.2135255100
45. Oppenheim AV RW Schafer Discrete-time signal processing Upper Saddle River (NJ): Prentice-Hall Inc 1999.
46. Song JH Kim JM Kim SH Kim HJ Lee JJ Sung MH Hwang SY Kim Sung Tae Comparison of the gene expression profiles of monocytic versus granulocytic lineages of HL-60 leukemia cell differentiation by DNA microarray analysis Life Sciences 2003, 73:1705-19. 10.1016/ S0024-3205(03)00515-0 12875902
47. Lee KH Chang MY Ahn JI Yu DH Jung SS Choi JH Noh YH Lee YS Ahn MJ Differential gene expression in retinoic acid-induced differentiation of acute promyelocytic leukemia cells, NB4 and HL-60 cells Biochemical and Biophysical Research Communications 2002, 296:1125-33. 10.1016/ S0006-291X(02)02043-0
48. Mattick J The Functional Genomics of Noncoding RNA Science 2005, 309:1527-8. 10.1126/science.1117806 16141063
49. The FANTOM Consortium The transcriptional landscape of the mammalian genome Science 2005, 309:1559-63. 10.1126/science.1112014 16141072
50. Bertone P Stolc V Royce TE Rozowsky JS Urban AE Zhu X Rinn JL Tongprasit W Samanta M Weissman S Gerstein M Snyder M Global Identification of Human Transcribed Sequences with Genome Tiling Arrays Science 2004, 306(5705):2242-6. 10.1126/science.1103388 15539566
51. Wightman B Burglin TR Gatto J Arasu P Ruvkun G Negative regulatory sequences in the lin-14 3′-untranslated region are necessary to generate a temporal switch during Caenorhabditis elegans development Genes Dev 1991, 5(10):1813-24. 10.1101/gad.5.10.1813 1916264
52. Integrated Genome Browser (IGB) is an open-source genome browser developed at Affymetrix http://www.affymetrix.com/support/developer/ downloads/TilingArrayTools/index.affx
53. Larsson O Wahlestedt C Timmons JA Considerations when using the significance analysis of microarrays (SAM) algorithm BMC Bioinformatics 2005, 6:129. 1173086 15921534 10.1186/1471-2105-6-129
54. Lee TI Rinaldi NJ Robert F Odom DT Bar-Joseph Z Gerber GK Hannett NM Harbison CT Thompson CM Simon I Zeitlinger J Jennings EG Murray HL Gordon DB Ren B Wyrick JJ Tagne JB Volkert TL Fraenkel E Gifford DK Young RA Transcriptional Regulatory Networks in Saccharomyces Cerevisiae Science 2002, 298:.
55. R is a freely available language and environment for statistical computing http://cran.rproject.org/