X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis

被引:49
作者
Yates, Tim [1 ]
Okoniewski, Michab J. [1 ]
Miller, Crispin J. [1 ]
机构
[1] Univ Manchester, Paterson Inst Canc Res, Bioinformat Grp, Christie Hosp Site, Manchester M20 4BX, Lancs, England
关键词
D O I
10.1093/nar/gkm779
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Affymetrix exon arrays aim to target every known and predicted exon in the human, mouse or rat genomes, and have reporters that extend beyond protein coding regions to other areas of the transcribed genome. This combination of increased coverage and precision is important because a substantial proportion of protein coding genes are predicted to be alternatively spliced, and because many non-coding genes are known also to be of biological significance. In order to fully exploit these arrays, it is necessary to associate each reporter on the array with the features of the genome it is targeting, and to relate these to gene and genome structure. X:Map is a genome annotation database that provides this information. Data can be browsed using a novel Google-maps based interface, and analysed and further visualized through an associated BioConductor package. The database can be found at http://xmap.picr.man.ac.uk.
引用
收藏
页码:D780 / D786
页数:7
相关论文
共 17 条
[1]  
*AFF WHIT, 2005, ALT TRANSCR AN METH
[2]  
Benson DA, 2010, NUCLEIC ACIDS RES, V38, pD46, DOI [10.1093/nar/gkp1024, 10.1093/nar/gkq1079, 10.1093/nar/gkl986, 10.1093/nar/gks1195, 10.1093/nar/gkw1070, 10.1093/nar/gkr1202, 10.1093/nar/gkn723, 10.1093/nar/gkx1094]
[3]   Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [J].
Birney, Ewan ;
Stamatoyannopoulos, John A. ;
Dutta, Anindya ;
Guigo, Roderic ;
Gingeras, Thomas R. ;
Margulies, Elliott H. ;
Weng, Zhiping ;
Snyder, Michael ;
Dermitzakis, Emmanouil T. ;
Stamatoyannopoulos, John A. ;
Thurman, Robert E. ;
Kuehn, Michael S. ;
Taylor, Christopher M. ;
Neph, Shane ;
Koch, Christoph M. ;
Asthana, Saurabh ;
Malhotra, Ankit ;
Adzhubei, Ivan ;
Greenbaum, Jason A. ;
Andrews, Robert M. ;
Flicek, Paul ;
Boyle, Patrick J. ;
Cao, Hua ;
Carter, Nigel P. ;
Clelland, Gayle K. ;
Davis, Sean ;
Day, Nathan ;
Dhami, Pawandeep ;
Dillon, Shane C. ;
Dorschner, Michael O. ;
Fiegler, Heike ;
Giresi, Paul G. ;
Goldy, Jeff ;
Hawrylycz, Michael ;
Haydock, Andrew ;
Humbert, Richard ;
James, Keith D. ;
Johnson, Brett E. ;
Johnson, Ericka M. ;
Frum, Tristan T. ;
Rosenzweig, Elizabeth R. ;
Karnani, Neerja ;
Lee, Kirsten ;
Lefebvre, Gregory C. ;
Navas, Patrick A. ;
Neri, Fidencio ;
Parker, Stephen C. J. ;
Sabo, Peter J. ;
Sandstrom, Richard ;
Shafer, Anthony .
NATURE, 2007, 447 (7146) :799-816
[4]   Discovery of tissue-specific exons using comprehensive human exon microarrays [J].
Clark, Tyson A. ;
Schweitzer, Anthony C. ;
Chen, Tina X. ;
Staples, Michelle K. ;
Lu, Gang ;
Wang, Hui ;
Williams, Alan ;
Blume, John E. .
GENOME BIOLOGY, 2007, 8 (04)
[5]   Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array [J].
Gardina, Paul J. ;
Clark, Tyson A. ;
Shimada, Brian ;
Staples, Michelle K. ;
Yang, Qing ;
Veitch, James ;
Schweitzer, Anthony ;
Awad, Tarif ;
Sugnet, Charles ;
Dee, Suzanne ;
Davies, Christopher ;
Williams, Alan ;
Turpaz, Yaron .
BMC GENOMICS, 2006, 7 (1)
[6]  
GENTLEMAN RC, 2004, BIOCONDUCTOR PROJECT
[7]   What is a gene, post-ENCODE? History and updated definition [J].
Gerstein, Mark B. ;
Bruce, Can ;
Rozowsky, Joel S. ;
Zheng, Deyou ;
Du, Jiang ;
Korbel, Jan O. ;
Emanuelsson, Olof ;
Zhang, Zhengdong D. ;
Weissman, Sherman ;
Snyder, Michael .
GENOME RESEARCH, 2007, 17 (06) :669-681
[8]   Ensembl 2007 [J].
Hubbard, T. J. P. ;
Aken, B. L. ;
Beal, K. ;
Ballester, B. ;
Caccamo, M. ;
Chen, Y. ;
Clarke, L. ;
Coates, G. ;
Cunningham, F. ;
Cutts, T. ;
Down, T. ;
Dyer, S. C. ;
Fitzgerald, S. ;
Fernandez-Banet, J. ;
Graf, S. ;
Haider, S. ;
Hammond, M. ;
Herrero, J. ;
Holland, R. ;
Howe, K. ;
Howe, K. ;
Johnson, N. ;
Kahari, A. ;
Keefe, D. ;
Kokocinski, F. ;
Kulesha, E. ;
Lawson, D. ;
Longden, I. ;
Melsopp, C. ;
Megy, K. ;
Meidl, P. ;
Overduin, B. ;
Parker, A. ;
Prlic, A. ;
Rice, S. ;
Rios, D. ;
Schuster, M. ;
Sealy, I. ;
Severin, J. ;
Slater, G. ;
Smedley, D. ;
Spudich, G. ;
Trevanion, S. ;
Vilella, A. ;
Vogel, J. ;
White, S. ;
Wood, M. ;
Cox, T. ;
Curwen, V. ;
Durbin, R. .
NUCLEIC ACIDS RESEARCH, 2007, 35 :D610-D617
[9]   Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments [J].
Johnson, JM ;
Edwards, S ;
Shoemaker, D ;
Schadt, EE .
TRENDS IN GENETICS, 2005, 21 (02) :93-102
[10]   Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays [J].
Johnson, JM ;
Castle, J ;
Garrett-Engele, P ;
Kan, ZY ;
Loerch, PM ;
Armour, CD ;
Santos, R ;
Schadt, EE ;
Stoughton, R ;
Shoemaker, DD .
SCIENCE, 2003, 302 (5653) :2141-2144