|
|
|
|
|
Tools and databases for analyzing genomic annotations
-
The Genomic HyperBrowser: inferential genomics at the sequence level,
Geir K Sandve, Sveinung Gundersen, Halfdan Rydbeck, Ingrid K Glad,
Lars Holden, Marit Holden, Knut Liestøl, Trevor Clancy, Egil
Ferkingstad, Morten Johansen, Vegard Nygaard, Eivind Tøstesen, Arnoldo
Frigessi, and Eivind Hovig.
Genome Biology 11:R121, 2010.
The Genomic HyperBrowser web
Supplementary material
Details of statistical tests
-
The UCSC Genome Browser database: update
2011,
Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS,
Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR,
Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM,
Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE,
Haussler D, and Kent WJ. Nucleic Acids Research, 2010 Oct 18.
Genome Browser Home
Table
Browser
Some analyses of ultraconserved elements
-
Ultraconserved elements in the human genome,
G Bejerano, M Pheasant, O Makunin, S Stephen, WJ Kent, JS Mattick, and
D Haussler.
Science 304:1321-1325, 2004.
-
Close sequence
comparisons are sufficient to identify human cis-regulatory
elements,
Shyam Prabhakar,
Francis Poulin,
Malak Shoukry,
Veena Afzal,
Edward M. Rubin,
Olivier Couronne, and
Len A. Pennacchio.
Genome Research 16: 855-863, 2006.
-
Ultraconservation identifies a small subset of extremely constrained
developmental enhancers,
Axel Visel, Shyam Prabhakar, Jennifer A Akiyama, Malak Shoukry,
Keith D Lewis, Amy Holt, Ingrid Plajzer-Frick, Veena Afzal, Edward
M Rubin, and Len A Pennacchio.
Nature Genetics 40:158-160, 2008.
-
Ultraconserved elements are associated with homeostatic control of
splicing regulators by alternative splicing and nonsense-mediated
decay,
Julie Z. Ni,
Leslie Grate,
John Paul Donohue,
Christine Preston,
Naomi Nobida,
Georgeann O'Brien,
Lily Shiue,
Tyson A. Clark,
John E. Blume, and
Manuel Ares, Jr.
Genes & Development 21:708-718, 2007.
-
Unproductive splicing of SR genes associated with highly conserved and
ultraconserved DNA elements,
Liana F. Lareau, Maki Inada, Richard E. Green, Jordan
C. Wengrod, and Steven E. Brenner.
Nature 446:926-929, 19 April 2007.
-
Algorithms
for Locating Extremely Conserved Elements in Multiple Sequence
Alignments,
Huei-Hun Elizabeth Tseng and Martin Tompa.
BMC Bioinformatics 10:432, 2009.
|
CSE Home 
