FactorY, a bioinformatic resource for genome-wide promoter analysis

被引：8
作者：
Guruceaga, Elizabeth [1 ]
Segura, Victor [1 ]
Corrales, Fernando J. [1 ]
Rubio, Angel [2 ]
机构：
[1] CIMA, Unit Proteom Genom & Bioinformat, Pamplona 31008, Spain
[2] Univ Navarra, Grp Bioinformat CEIT & Tecnun, San Sebastian 20009, Spain
来源：
COMPUTERS IN BIOLOGY AND MEDICINE | 2009年 / 39卷 / 04期
关键词：
Genomics; Microarrays; Transcriptional regulation; Sequence analysis; Gene ontology; EXPRESSION;
D O I：
10.1016/j.compbiomed.2009.01.008
中图分类号：
Q [生物科学];
学科分类号：
07 ; 0710 ; 09 ;
摘要：
The interpretation of the complex molecular descriptions generated by high-throughput gene expression technologies is still challenging. The development of new tools to identify common regulatory mechanisms involved in the control of the expression of a set of co-expressed genes. might enhance our capacity to extract functional information from genomic data sets. Here we present FactorY, a website that allows identification of enriched transcription factor binding sites (TFBSs) in the proximal promoter of a cluster of genes, as well as functional interpretation, and intuitive visualization of the results. (c) 2009 Elsevier Ltd. All rights reserved.
引用
收藏
页码：385 / 387
页数：3
相关论文
共 14 条
  • [1] Toucan:: deciphering the cis-regulatory logic of coregulated genes
    Aerts, S
    Thijs, G
    Coessens, B
    Staes, M
    Moreau, Y
    Moor, BD
    [J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (06) : 1753 - 1764
  • [2] A systematic model to predict transcriptional regulatory mechanisms based on over representation of transcription factor binding profiles
    Chang, LW
    Nagarajan, R
    Magee, JA
    Milbrandt, J
    Stormo, GD
    [J]. GENOME RESEARCH, 2006, 16 (03) : 405 - 413
  • [3] Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
    Cheng, J
    Kapranov, P
    Drenkow, J
    Dike, S
    Brubaker, S
    Patel, S
    Long, J
    Stern, D
    Tammana, H
    Helt, G
    Sementchenko, V
    Piccolboni, A
    Bekiranov, S
    Bailey, DK
    Ganesh, M
    Ghosh, S
    Bell, I
    Gerhard, DS
    Gingeras, TR
    [J]. SCIENCE, 2005, 308 (5725) : 1149 - 1154
  • [4] Evolution of transcription factor binding sites in mammalian gene regulatory regions: Conservation and turnover
    Dermitzakis, ET
    Clark, AG
    [J]. MOLECULAR BIOLOGY AND EVOLUTION, 2002, 19 (07) : 1114 - 1121
  • [5] Cluster analysis and display of genome-wide expression patterns
    Eisen, MB
    Spellman, PT
    Brown, PO
    Botstein, D
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (25) : 14863 - 14868
  • [6] *ENS CONS, 2007, NUCLEIC ACIDS RES, V35, P610
  • [7] EnsMart: A generic system for fast and flexible access to biological data
    Kasprzyk, A
    Keefe, D
    Smedley, D
    London, D
    Spooner, W
    Melsopp, C
    Hammond, M
    Rocca-Serra, P
    Cox, T
    Birney, E
    [J]. GENOME RESEARCH, 2004, 14 (01) : 160 - 169
  • [8] THE ACCURACY OF PEIZER APPROXIMATIONS TO THE HYPERGEOMETRIC DISTRIBUTION, WITH COMPARISONS TO SOME OTHER APPROXIMATIONS
    LING, RF
    PRATT, JW
    [J]. JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 1984, 79 (385) : 49 - 60
  • [9] TRANSFAC® and its module TRANSCompel®:: transcriptional gene regulation in eukaryotes
    Matys, V.
    Kel-Margoulis, O. V.
    Fricke, E.
    Liebich, I.
    Land, S.
    Barre-Dirrie, A.
    Reuter, I.
    Chekmenev, D.
    Krull, M.
    Hornischer, K.
    Voss, N.
    Stegmaier, P.
    Lewicki-Potapov, B.
    Saxel, H.
    Kel, A. E.
    Wingender, E.
    [J]. NUCLEIC ACIDS RESEARCH, 2006, 34 : D108 - D110
  • [10] Estimation and control of multiple testing error rates for microarray studies
    Pounds, Stanley B.
    [J]. BRIEFINGS IN BIOINFORMATICS, 2006, 7 (01) : 25 - 36
12