GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs

被引:18
作者
Jegga, Anil G.
Chen, Jing
Gowrisankar, Sivakumar
Deshmukh, Mrunal A.
Gudivada, RangaChandra
Kong, Sue
Kaimal, Vivek
Aronow, Bruce J.
机构
[1] Childrens Hosp, Med Ctr, Div Biomed Informat, Cincinnati, OH 45229 USA
[2] Univ Cincinnati, Coll Med, Dept Pediat, Cincinnati, OH 45229 USA
[3] Univ Cincinnati, Dept Biomed Engn, Cincinnati, OH 45229 USA
关键词
D O I
10.1093/nar/gkl1011
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
Transcriptional cis-regulatory control regions frequently are found within non-coding DNA segments conserved across multi-species gene orthologs. Adopting a systematic gene-centric pipeline approach, we report here the development of a web-accessible database resource-GenomeTraFac (http://genometrafac.cchmc.org)-that allows genome-wide detection and characterization of compositionally similar cis-clusters that occur in gene orthologs between any two genomes for both microRNA genes as well as conventional RNA-encoding genes. Each ortholog gene pair can be scanned to visualize overall conserved sequence regions, and within these, the relative density of conserved cis-element motif clusters form graph peak structures. The results of these analyses can be mined en masse to identify most frequently represented cis-motifs in a list of genes. The system also provides a method for rapid evaluation and visualization of gene model-consistency between orthologs, and facilitates consideration of the potential impact of sequence variation in conserved non-coding regions to impact complex cis-element structures. Using the mouse and human genomes via the NCBI Reference Sequence database and the Sanger Institute miRBase, the system demonstrated the ability to identify validated transcription factor targets within promoter and distal genomic regulatory regions of both conventional and microRNA genes.
引用
收藏
页码:D116 / D121
页数:6
相关论文
共 34 条
[11]  
Hamosh A, 2005, NUCLEIC ACIDS RES, V33, pD514
[12]   CisMols Analyzer:: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes [J].
Jegga, AG ;
Gupta, A ;
Gowrisankar, S ;
Deshmukh, MA ;
Connolly, S ;
Finley, K ;
Aronow, BJ .
NUCLEIC ACIDS RESEARCH, 2005, 33 :W408-W411
[13]   Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes [J].
Jegga, AG ;
Sherwood, SP ;
Carman, JW ;
Pinski, AT ;
Phillips, JL ;
Pestian, JP ;
Aronow, BJ .
GENOME RESEARCH, 2002, 12 (09) :1408-1417
[14]   The UCSC Genome Browser Database [J].
Karolchik, D ;
Baertsch, R ;
Diekhans, M ;
Furey, TS ;
Hinrichs, A ;
Lu, YT ;
Roskin, KM ;
Schwartz, M ;
Sugnet, CW ;
Thomas, DJ ;
Weber, RJ ;
Haussler, D ;
Kent, WJ .
NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :51-54
[15]   Evaluation of MYC E-box phylogenetic footprints in glycolytic genes by chromatin immunoprecipitation assays [J].
Kim, JW ;
Zeller, KI ;
Wang, Y ;
Jegga, AG ;
Aronow, BJ ;
O'Donnell, KA ;
Dang, CV .
MOLECULAR AND CELLULAR BIOLOGY, 2004, 24 (13) :5923-5936
[16]   Transcriptional regulatory networks in Saccharomyces cerevisiae [J].
Lee, TI ;
Rinaldi, NJ ;
Robert, F ;
Odom, DT ;
Bar-Joseph, Z ;
Gerber, GK ;
Hannett, NM ;
Harbison, CT ;
Thompson, CM ;
Simon, I ;
Zeitlinger, J ;
Jennings, EG ;
Murray, HL ;
Gordon, DB ;
Ren, B ;
Wyrick, JJ ;
Tagne, JB ;
Volkert, TL ;
Fraenkel, E ;
Gifford, DK ;
Young, RA .
SCIENCE, 2002, 298 (5594) :799-804
[17]  
Lenhard Boris, 2003, J Biol, V2, P13, DOI 10.1186/1475-4924-2-13
[18]   Dissecting the transcription networks of a cell using computational genomics [J].
Li, H ;
Wang, W .
CURRENT OPINION IN GENETICS & DEVELOPMENT, 2003, 13 (06) :611-616
[19]   rVista for comparative sequence-based discovery of functional transcription factor binding sites [J].
Loots, GG ;
Ovcharenko, I ;
Pachter, L ;
Dubchak, I ;
Rubin, EM .
GENOME RESEARCH, 2002, 12 (05) :832-839
[20]   Deciphering genetic regulatory codes: A challenge for functional genomics [J].
Michelson, AM .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (02) :546-548