ENCODE

The ENCyclopedia Of DNA Elements (ENCODE) Project, funded by the National Human Genome Research Institute, is a public research consortium whose goal is to identify all the functional elements in the human genome sequence.  The Myers lab has been a member of the ENCODE Consortium since it was launched in 2003, first participating in the pilot project aimed at annotating 1% of the human genome and then joining the full genome effort in 2007.  In collaboration with Barbara Wold’s lab at Caltech we developed or adapted protocols for ChIP-seq, RNA-seq, and DNA methylation.  We have generated hundreds of genome-wide datasets that measure transcription factor binding sites, RNA expression, DNA methylation, and genotyping in many different kinds of cells.  All of our data are publicly available and can be searched, downloaded, and browsed through the ENCODE Experiment Matrix on the UCSC genome browser or through each data track listed below.

 

ENCODE – HudsonAlpha – ChIP-seq

ENCODE – HudsonAlpha – RNA-seq

ENCODE – Caltech – RNA-seq

ENCODE – HudsonAlpha – Methylation

ENCODE – HudsonAlpha – Genotyping

 

The ENCODE data, protocols, and analysis have been produced by many dedicated research assistants, graduate students, postdoctoral fellows, computational biologists, and staff scientists.  For questions regarding the Myers lab ENCODE data, please contact Dr. Flo Pauli.

 

Related Publications

Reddy, T. E., Gertz, J., Pauli, F., Kucera, K. S., Newberry, K. M., Marinov, G. K., Mortazavi, A., Williams, B. A., Wold, B., Willard, H. F. and Myers, R. M.  (2012).  Effects of sequence variation on differential allelic transcription factor occupancy and gene expression.  Genome Res.  Feb 2. [Epub ahead of print].  PMID: 22300769.  PMCID:  PMC3337432 [Available on 2012/11/1]. See Research Highlight in Nature Reviews Genetics. doi:10.1038/nrg3219. PDF

Gertz, J., Varley, K., Reddy, T., Bowling, K., Pauli, F., Parker, S., Kucera, K., Willard, H. and Myers, R. M.  (2011).  Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.  PLoS Genetics.  7: e1002228. Epub Aug 11.  PMID: 21852959.  PMCID: PMC3154961. PDF

ENCODE Project Consortium.  (2011).  A user’s guide to the Encyclopedia of DNA Elements (ENCODE).  PLoS Biol.  9: e1001046.  PMID: 21526222.  PMCID: PMC3079585. PDF

Brunner, A. L.,Johnson, D. S., Kim, S. W., Valouev, A., Reddy, T. E., Neff, N. F., Anton, E., Medina, C., Nguyen. L., Chiao, E., Oyolu, C. B., Schroth, G. P., Absher, D., Baker, J. C. and Myers, R. M.  (2009).  Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver.  Genome Res. 19: 1044-1056. PMID: 19273619.  PMCID: PMC2694474. PDF

Valouev, A., Johnson, D. S., Sundquist, A., Medina, C., Anton, E., Batzoglou, S., Myers, R. M. and Sidow, A.  (2008). Genome-wide analysis of transcription factor binding sites based on ChIP-seq data.  Nat. Methods.  5: 829-834.  PMID: 19160518.  PMCID: PMC2917543.  PDF

Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nussbaum, C., Myers, R. M., Brown, M., Li, W. and Liu, X. S.  (2008).  Model-based analysis of ChIP-Seq (MACS). Genome Biol.  9: R137.  PMID: 18798982.  PMCID: PMC2592715. PDF

Ji, H., Jiang, H., Ma, W., Johnson, D. S., Myers, R. M., and Wong, W. H.  (2008).  An integrated system CisGenome for analyzing ChIP-chip and ChIP-seq data.  Nat. Biotechnol. 26: 1293-1300.  PMID: 18978777.  PMCID: PMC2596672. PDF

Johnson, D. S., Li, W., Gordon, D. B., Bhattacharjee, A., Curry, B., Ghosh, J., Brizuela, L., Carroll, J. S., Brown, M., Flicek, P., Koch, C., Dunham, I., Bieda, M., Xu, X., Farnham, P., Kapranov, P., Nix, D. A., Gingeras, T., Zhang, X., Holster, H., Jing, N., Green, R., Song, J., McCuine, S. A., Anton, E., Nguyen, L., Trinklein, N. D., Ye, Z., Ching, K., Hawkins, D., Ren, B., Scacheri1, P. C., Rozowsky, J., Karpikov, A., Euskirchen, G., Weissman, S., Gerstein, M., Snyder, M., Yang, A., Moqtaderi, Z., Hirsch, H., Shulha, H. P., Fu, Y., Weng, Z., Struhl, K., Myers, R. M., Lieb, J. D., and Liu, X. S. (2008).  Systematic evaluation of variability in simulated ChIP-chip experiments.  Genome Res.  18: 393-403. PMID: 18258921.  PMCID: PMC2259103. PDF

ENCODE Project Consortium. (2007).  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.  Nature.  447:  799-816.  See also:  News and Views by John M. Greally.  Nature.  447: 782-783.  PMID: 17571346.  PMCID: PMC2212820. PDF

Denoeud, F., Kapranov, P., Ucla, C., Frankish, A., Castelo, R., Drenkow, J., Lagarde, J., Alioto, T., Manzano, C., Chrast, J., Dike, S., Wyss, C., Henrichsen, C. N., Holroyd, N., Dickson, M. C., Taylor, R., Hance, Z., Foissac, S., Myers, R. M., Rogers, J., Hubbard, T., Harrow, J., Guigo, R., Gingeras, T. R., Antonarakis, S. E. and Reymond, A.  (2007).  Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions.  Genome Res.  17: 746-759.  PMID: 17567994.  PMCID: PMC1891335. PDF

*Johnson, D. S., *Mortazavi, A., Myers, R. M. and Wold, B.  (2007).  Genome-wide mapping of in vivo protein DNA interactions.  Science. 316:  1497-1502. (*co-first authors).  PMID: 17540862.  [PubMed - indexed for MEDLINE].  See also: Perspective by Stanley Fields.  Science.  316: 1441-1442. PDF

ENCODE Project Consortium.  (2004).  The ENCODE (ENCyclopedia Of DNA Elements) Project.  Science.  306: 636-640.  PMID: 15499007. PDF