Automated computational analysis of genome-wide DNA methylation profiling data from HELP-tagging assays

Methods in Molecular Biology

Volumn 815, Issue , 2012, Pages 79-87

  Jing, Qiang ^a   McLellan, Andrew ^a   Greally, John M ^a   Suzuki, Masako ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

Bioinformatics; Computational analysis; DNA methylation; Pipeline

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; CPG ISLAND; DNA METHYLATION; DNA PROBE; GENE LIBRARY; GENETIC EPIGENESIS; LABORATORY AUTOMATION; METHODOLOGY; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; SYNTHESIS;

ALGORITHMS; AUTOMATION, LABORATORY; BASE SEQUENCE; COMPUTER SIMULATION; CPG ISLANDS; DNA METHYLATION; DNA PROBES; EPIGENESIS, GENETIC; GENOMIC LIBRARY; MODELS, GENETIC; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 84555178791     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-424-7_7     Document Type: Article

References (17)

1. Bird, A. P., and Wolffe, A. P. (1999) Methylationinduced repression-belts, braces, and chromatin, Cell 99, 451-454.
2. Li, E., Bestor, T. H., and Jaenisch, R. (1992) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality, Cell 69, 915-926.
3. Okano, M., Bell, D. W., Haber, D. A., and Li, E. (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development, Cell 99, 247-257. (Pubitemid 29519904)
4. Costello, J. F., Fruhwald, M. C., Smiraglia, D. J., Rush, L. J., Robertson, G. P., Gao, X., Wright, F. A., Feramisco, J. D., Peltomaki, P., Lang, J. C., Schuller, D. E., Yu, L., Bloomfield, C. D., Caligiuri, M. A., Yates, A., Nishikawa, R., Su Huang, H., Petrelli, N. J., Zhang, X., O'Dorisio, M. S., Held, W. A., Cavenee, W. K., and Plass, C. (2000) Aberrant CpGisland methylation has non-random and tumour-type-specific patterns, Nat Genet 24, 132-138. (Pubitemid 30094712)
5. Greger, V., Passarge, E., Hopping, W., Messmer, E., and Horsthemke, B. (1989) Epigenetic changes may contribute to the formation and spontaneous regression of retinoblastoma, Hum Genet 83, 155-158. (Pubitemid 19234564)
6. Dobrovic, A., and Simpfendorfer, D. (1997) Methylation of the BRCA1 gene in sporadic breast cancer, Cancer Res 57, 3347-3350. (Pubitemid 27355472)
7. Gebhard, C., Schwarzfischer, L., Pham, T. H., Schilling, E., Klug, M., Andreesen, R., and Rehli, M. (2006) Genome-wide profiling of CpG methylation identifies novel targets of aberrant hypermethylation in myeloid leukemia, Cancer Res 66, 6118-6128.
8. Akiyama, Y., Watkins, N., Suzuki, H., Jair, K. W., van Engeland, M., Esteller, M., Sakai, H., Ren, C. Y., Yuasa, Y., Herman, J. G., and Baylin, S. B. (2003) GATA-4 and GATA-5 transcription factor genes and potential downstream antitumor target genes are epigenetically silenced in colorectal and gastric cancer, Mol Cell Biol 23, 8429-8439. (Pubitemid 37433351)
9. Suzuki, M., Sato, S., Arai, Y., Shinohara, T., Tanaka, S., Greally, J. M., Hattori, N., and Shiota, K. (2007) A new class of tissue-specifically methylated regions involving entire CpG islands in the mouse, Genes Cells 12, 1305-1314. (Pubitemid 350215135)
10. Suzuki, M. M., and Bird, A. (2008) DNA methylation landscapes: provocative insights from epigenomics, Nat Rev Genet 9, 465-476. (Pubitemid 351693975)
11. Backdahl, L., Herberth, M., Wilson, G., Tate, P., Campos, L. S., Cortese, R., Eckhardt, F., and Beck, S. (2009) Gene body methylation of the dimethylarginine dimethylamino-hydrolase 2 (Ddah2) gene is an epigenetic biomarker for neural stem cell differentiation, Epigenetics 4, 248-254.
12. Ball, M. P., Li, J. B., Gao, Y., Lee, J. H., LeProust, E. M., Park, I. H., Xie, B., Daley, G. Q., and Church, G. M. (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells, Nat Biotechnol 27, 361-368.
13. Suzuki, M., Jing, Q., Lia, D., Pascual, M., McLellan, A., and Greally, J. M. (2010) Optimized design and data analysis of tag-based cytosine methylation assays, Genome Biol 11, R36.
14. Illumina. (2010) CASAVA Software Version 1.7 User Guide, Illumina Inc.
15. Cox, A. J. (unpublished) ELAND: Efficient Local Alignment of Nucleotide Data.
16. Langmead, B., Trapnell, C., Pop, M., and Salzberg, S. L. (2009) Ultrafast and memoryefficient alignment of short DNA sequences to the human genome, Genome Biol 10, R25.
17. Aitchison, J., and Brown, J. A. C. (1957) The lognormal distribution, with special reference to its uses in economics, University Press, Cambridge.