Deciphering ENCODE

Trends in Genetics

Volumn 32, Issue 4, 2016, Pages 238-249

  Diehl, Adam G ^a   Boyle, Alan P ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

ChIP seq; DNase seq; ENCODE; Gene regulation; Genomics; RNA seq

Indexed keywords

DNA;

DATA ANALYSIS; GENE CONTROL; GENE SEQUENCE; GENETIC ANALYSIS; GENOME; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; GENETIC DATABASE; GENOMICS; HUMAN; INTERNET;

DATABASES, GENETIC; GENOMICS; HUMANS; INTERNET; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84959466643     PISSN: 01689525     EISSN: 13624555     Source Type: Journal    
DOI: 10.1016/j.tig.2016.02.002     Document Type: Review

References (34)

1. The ENCODE Project Consortium A User's Guide to the Encyclopedia of DNA Elements 2011, ENCODE.
2. Pazin M.J. Using the ENCODE resource for functional annotation of genetic variants. Cold Spring Harb. Protoc. 2015, 2015:522-536.
3. The ENCODE Project Consortium Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816.
4. The ENCODE Project Consortium The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004, 306:636-640.
5. Harrow J., et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012, 22:1760-1774.
6. Mouse ENCODE Consortium An encyclopedia of mouse DNA elements (mouse ENCODE). Genome Biol. 2012, 13:418.
7. Gerstein M.B., et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 2010, 330:1775-1787.
8. modENCODE Consortium Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2010, 330:1787-1797.
9. Boyle A.P., et al. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 2012, 22:1790-1797.
10. Cunningham F., et al. Ensembl 2015. Nucleic Acids Res. 2015, 43:D662-D669.
11. Rosenbloom K.R., et al. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res. 2010, 38:D620-D625.
12. Thomas D.J., et al. The ENCODE Project at UC Santa Cruz. Nucleic Acids Res. 2007, 35:D663-D667.
13. Yates A., et al. The Ensembl REST API: Ensembl data for any language. Bioinformatics 2015, 31:143-145.
14. Li S., et al. Detecting and correcting systematic variation in large-scale RNA sequencing data. Nat. Biotechnol. 2014, 32:888-895.
15. Gilad Y., Mizrahi-Man O. A reanalysis of mouse ENCODE comparative gene expression data. F1000Res 2015, 4:121.
16. Robinson M.D., Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010, 11:R25.
17. Leek J.T., et al. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat. Rev. Genet. 2010, 11:733-739.
18. Meyer C.A., Liu X.S. Identifying and mitigating bias in next-generation sequencing methods for chromatin biology. Nat. Rev. Genet. 2014, 15:709-721.
19. Dillies M.A., et al. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief Bioinformatics 2013, 14:671-683.
20. Taub M.A., et al. Overcoming bias and systematic errors in next generation sequencing data. Genome Med. 2010, 2:87.
21. Risso D., et al. GC-content normalization for RNA-Seq data. BMC Bioinformatics 2011, 12:480.
22. Leek J.T., et al. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics 2012, 28:882-883.
23. Robinson M.D., et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26:139-140.
24. Johnson W.E., et al. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007, 8:118-127.
25. Guenther C.A., et al. A molecular basis for classic blond hair color in Europeans. Nat. Genet. 2014, 46:748-752.
26. Ward L.D., Kellis M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 2012, 40:D930-D934.
27. Guo Y., et al. CRISPR inversion of CTCF sites alters genome topology and enhancer/promoter function. Cell 2015, 162:900-910.
28. Nichols M.H., Corces V.G. A CTCF code for 3D genome architecture. Cell 2015, 162:703-705.
29. Corradin O., et al. Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits. Genome Res. 2013, 24:1-13.
30. Eddy S.R. The C-value paradox, junk DNA and ENCODE. Curr. Biol. 2012, 22:R898-R899.
31. Doolittle W.F. Is junk DNA bunk? A critique of ENCODE. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:5294-5300.
32. Eddy S.R. The ENCODE project: missteps overshadowing a success. Curr. Biol. 2013, 23:R259-R261.
33. Graur D., et al. On the immortality of television sets: 'function' in the human genome according to the evolution-free gospel of ENCODE. Genome Biol. Evol. 2013, 5:578-590.
34. Lin S., et al. Comparison of the transcriptional landscapes between human and mouse tissues. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:17224-17229.