Comparative and functional analysis of cardiovascular-related genes

被引:2
作者
Cheng, JF
Pennacchio, LA
机构
[1] Lawrence Berkeley Lab, Dept Genome Sci, Berkeley, CA 94720 USA
[2] US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA
关键词
apolipoprotein; BAC; cardiovascular; comparative genomics; gene regulation; orthology; PGA; phylogenetic shadowing; VISTA;
D O I
10.1517/phgs.4.5.571.23794
中图分类号
R9 [药学];
学科分类号
1007 ;
摘要
The ability to detect putative cis-regulatory elements in cardiovascular-related genes has been accelerated by the availability of genomic sequence data from numerous vertebrate species and the recent development of comparative genomic tools. This improvement is anticipated to lead to a better understanding of the complex regulatory architecture of cardiovascular (CV) genes and how genetic variants in these non-coding regions can potentially play a role in cardiovascular disease. This manuscript reviews a recently established database dedicated to the comparative sequence analysis of 250 human CV genes of known importance, 37 of which currently contain sequence comparison data for organisms beyond those of human, mouse and rat. These data have provided a glimpse into the variety of possible insights from deep vertebrate sequence comparisons and the identification of putative gene regulatory elements.
引用
收藏
页码:571 / 582
页数:12
相关论文
共 34 条
  • [1] Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes
    Aparicio, S
    Chapman, J
    Stupka, E
    Putnam, N
    Chia, J
    Dehal, P
    Christoffels, A
    Rash, S
    Hoon, S
    Smit, A
    Gelpke, MDS
    Roach, J
    Oh, T
    Ho, IY
    Wong, M
    Detter, C
    Verhoef, F
    Predki, P
    Tay, A
    Lucas, S
    Richardson, P
    Smith, SF
    Clark, MS
    Edwards, YJK
    Doggett, N
    Zharkikh, A
    Tavtigian, SV
    Pruss, D
    Barnstead, M
    Evans, C
    Baden, H
    Powell, J
    Glusman, G
    Rowen, L
    Hood, L
    Tan, YH
    Elgar, G
    Hawkins, T
    Venkatesh, B
    Rokhsar, D
    Brenner, S
    [J]. SCIENCE, 2002, 297 (5585) : 1301 - 1310
  • [2] Human and mouse gene structure: Comparative analysis and application to exon prediction
    Batzoglou, S
    Pachter, L
    Mesirov, JP
    Berger, B
    Lander, ES
    [J]. GENOME RESEARCH, 2000, 10 (07) : 950 - 958
  • [3] Phylogenetic shadowing of primate sequences to find functional regions of the human genome
    Boffelli, D
    McAuliffe, J
    Ovcharenko, D
    Lewis, KD
    Ovcharenko, I
    Pachter, L
    Rubin, EM
    [J]. SCIENCE, 2003, 299 (5611) : 1391 - 1394
  • [4] AVID: A global alignment program
    Bray, N
    Dubchak, I
    Pachter, L
    [J]. GENOME RESEARCH, 2003, 13 (01) : 97 - 102
  • [5] LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
    Brudno, M
    Do, CB
    Cooper, GM
    Kim, MF
    Davydov, E
    Green, ED
    Sidow, A
    Batzoglou, S
    [J]. GENOME RESEARCH, 2003, 13 (04) : 721 - 731
  • [6] Glocal alignment: finding rearrangements during alignment
    Brudno, Michael
    Malde, Sanket
    Poliakov, Alexander
    Do, Chuong B.
    Couronne, Olivier
    Dubchak, Inna
    Batzoglou, Serafim
    [J]. BIOINFORMATICS, 2003, 19 : i54 - i62
  • [7] Strategies and tools for whole-genome alignments
    Couronne, O
    Poliakov, A
    Bray, N
    Ishkhanov, T
    Ryaboy, D
    Rubin, E
    Pachter, L
    Dubchak, I
    [J]. GENOME RESEARCH, 2003, 13 (01) : 73 - 80
  • [8] Human chromosome 19 and related regions in mouse: Conservative and lineage-specific evolution
    Dehal, P
    Predki, P
    Olsen, AS
    Kobayashi, A
    Folta, P
    Lucas, S
    Land, M
    Terry, A
    Zhou, CLE
    Rash, S
    Zhang, Q
    Gordon, L
    Kim, J
    Elkin, C
    Pollard, MJ
    Richardson, P
    Rokhsar, D
    Uberbacher, E
    Hawkins, T
    Branscomb, E
    Stubbs, L
    [J]. SCIENCE, 2001, 293 (5527) : 104 - 111
  • [9] Numerous potentially functional but non-genic conserved sequences on human chromosome 21
    Dermitzakis, ET
    Reymond, A
    Lyle, R
    Scamuffa, N
    Ucla, C
    Deutsch, S
    Stevenson, BJ
    Flegel, V
    Bucher, P
    Jongeneel, CV
    Antonarakis, SE
    [J]. NATURE, 2002, 420 (6915) : 578 - 582
  • [10] Cross-species sequence comparisons: A review of methods and available resources
    Frazer, KA
    Elnitski, L
    Church, DM
    Dubchak, I
    Hardison, RC
    [J]. GENOME RESEARCH, 2003, 13 (01) : 1 - 12