STUDY DESIGNS Studying and modelling dynamic biological processes using time-series gene expression data

被引：339
作者：
Bar-Joseph, Ziv [1 ,2 ]
Gitter, Anthony [3 ]
Simon, Itamar [4 ]
机构：
[1] Carnegie Mellon Univ, Sch Comp Sci, Lane Ctr Computat Biol, Pittsburgh, PA 15213 USA
[2] Carnegie Mellon Univ, Sch Comp Sci, Machine Learning Dept, Pittsburgh, PA 15213 USA
[3] Carnegie Mellon Univ, Sch Comp Sci, Dept Comp Sci, Pittsburgh, PA 15213 USA
[4] Hebrew Univ Jerusalem, Hadassah Med Sch, Dept Microbiol & Mol Genet, IMRIC, IL-91010 Jerusalem, Israel
来源：
NATURE REVIEWS GENETICS | 2012年 / 13卷 / 08期
基金：
欧洲研究理事会; 美国国家卫生研究院; 以色列科学基金会;
关键词：
NETWORK COMPONENT ANALYSIS; HUMAN CELL-CYCLE; RNA-SEQ; TRANSCRIPTIONAL CONTROL; REGULATORY NETWORKS; MICROARRAY ANALYSIS; BAYESIAN-ESTIMATION; CLUSTER-ANALYSIS; REVEALS; RESPONSES;
D O I：
10.1038/nrg3244
中图分类号：
Q3 [遗传学];
学科分类号：
071007 ; 090102 ;
摘要：
Biological processes are often dynamic, thus researchers must monitor their activity at multiple time points. The most abundant source of information regarding such dynamic activity is time-series gene expression data. These data are used to identify the complete set of activated genes in a biological process, to infer their rates of change, their order and their causal effects and to model dynamic systems in the cell. In this Review we discuss the basic patterns that have been observed in time-series experiments, how these patterns are combined to form expression programs, and the computational analysis, visualization and integration of these data to infer models of dynamic biological systems.
引用
收藏
页码：552 / 564
页数：13
相关论文
共 116 条
  • [1] Network motifs: theory and experimental approaches
    Alon, Uri
    [J]. NATURE REVIEWS GENETICS, 2007, 8 (06) : 450 - 461
  • [2] A module of negative feedback regulators defines growth factor signaling
    Amit, Ido
    Citri, Ami
    Shay, Tal
    Lu, Yiling
    Katz, Menachem
    Zhang, Fan
    Tarcic, Gabi
    Siwak, Doris
    Lahad, John
    Jacob-Hirsch, Jasmine
    Amariglio, Ninette
    Vaisman, Nora
    Segal, Eran
    Rechavi, Gideon
    Alon, Uri
    Mills, Gordon B.
    Domany, Eytan
    Yarden, Yosef
    [J]. NATURE GENETICS, 2007, 39 (04) : 503 - 512
  • [3] Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses
    Amit, Ido
    Garber, Manuel
    Chevrier, Nicolas
    Leite, Ana Paula
    Donner, Yoni
    Eisenhaure, Thomas
    Guttman, Mitchell
    Grenier, Jennifer K.
    Li, Weibo
    Zuk, Or
    Schubert, Lisa A.
    Birditt, Brian
    Shay, Tal
    Goren, Alon
    Zhang, Xiaolan
    Smith, Zachary
    Deering, Raquel
    McDonald, Rebecca C.
    Cabili, Moran
    Bernstein, Bradley E.
    Rinn, John L.
    Meissner, Alex
    Root, David E.
    Hacohen, Nir
    Regev, Aviv
    [J]. SCIENCE, 2009, 326 (5950) : 257 - 263
  • [4] Gene expression during the life cycle of Drosophila melanogaster
    Arbeitman, MN
    Furlong, EEM
    Imam, F
    Johnson, E
    Null, BH
    Baker, BS
    Krasnow, MA
    Scott, MP
    Davis, RW
    White, KP
    [J]. SCIENCE, 2002, 297 (5590) : 2270 - 2275
  • [5] An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation)
    Aryee, Martin J.
    Gutierrez-Pabello, Jose A.
    Kramnik, Igor
    Maiti, Tapabrata
    Quackenbush, John
    [J]. BMC BIOINFORMATICS, 2009, 10
  • [6] Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
    Bansal, M
    Della Gatta, G
    di Bernardo, D
    [J]. BIOINFORMATICS, 2006, 22 (07) : 815 - 822
  • [7] Continuous representations of time-series gene expression data
    Bar-Joseph, Z
    Gerber, GK
    Gifford, DK
    Jaakkola, TS
    Simon, I
    [J]. JOURNAL OF COMPUTATIONAL BIOLOGY, 2003, 10 (3-4) : 341 - 356
  • [8] Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes
    Bar-Joseph, Z
    Gerber, G
    Simon, L
    Gifford, DK
    Jaakkola, TS
    Jaakkola, TS
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (18) : 10146 - 10151
  • [9] Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells
    Bar-Joseph, Ziv
    Siegfried, Zahava
    Brandeis, Michael
    Brors, Benedikt
    Lu, Yong
    Eils, Roland
    Dynlacht, Brian D.
    Simon, Itamar
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (03) : 955 - 960
  • [10] Deconvolving cell cycle expression data with complementary information
    Bar-Joseph, Ziv
    Farkash, Shlomit
    Gifford, David K.
    Simon, Itamar
    Rosenfeld, Roni
    [J]. BIOINFORMATICS, 2004, 20 : 23 - 30
12345678910