Integrated approaches to uncovering transcription regulatory networks in mammalian cells

Kai Tan; Jesper Tegner; Timothy Ravasi

doi:10.1016/j.ygeno.2007.11.005

Integrated approaches to uncovering transcription regulatory networks in mammalian cells

Kai Tan^*, Jesper Tegner, Timothy Ravasi

^*Corresponding author for this work

Research output: Contribution to journal › Review article › peer-review

33 Scopus citations

Abstract

Integrative systems biology has emerged as an exciting research approach in molecular biology and functional genomics that involves the integration of genomics, proteomics, and metabolomics datasets. These endeavors establish a systematic paradigm by which to interrogate, model, and iteratively refine our knowledge of the regulatory events within a cell. Here we review the latest technologies available to collect high-throughput measurements of a cellular state as well as the most successful methods for the integration and interrogation of these measurements. In particular we will focus on methods available to infer transcription regulatory networks in mammals.

Original language	English (US)
Pages (from-to)	219-231
Number of pages	13
Journal	Genomics
Volume	91
Issue number	3
DOIs	https://doi.org/10.1016/j.ygeno.2007.11.005
State	Published - Mar 2008
Externally published	Yes

Keywords

Bioinformatics
Cellular networks
ChIp-chip
Dynamics
Gene expression
Gene networks
Genomics
Networks
Personalized medicine
Protein interaction maps
Protein-protein interaction networks
Systems biology
Systems medicine
Transcriptional networks

ASJC Scopus subject areas

Genetics

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10.1016/j.ygeno.2007.11.005

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title = "Integrated approaches to uncovering transcription regulatory networks in mammalian cells",

abstract = "Integrative systems biology has emerged as an exciting research approach in molecular biology and functional genomics that involves the integration of genomics, proteomics, and metabolomics datasets. These endeavors establish a systematic paradigm by which to interrogate, model, and iteratively refine our knowledge of the regulatory events within a cell. Here we review the latest technologies available to collect high-throughput measurements of a cellular state as well as the most successful methods for the integration and interrogation of these measurements. In particular we will focus on methods available to infer transcription regulatory networks in mammals.",

keywords = "Bioinformatics, Cellular networks, ChIp-chip, Dynamics, Gene expression, Gene networks, Genomics, Networks, Personalized medicine, Protein interaction maps, Protein-protein interaction networks, Systems biology, Systems medicine, Transcriptional networks",

author = "Kai Tan and Jesper Tegner and Timothy Ravasi",

note = "Funding Information: K.T. was funded by a postdoctoral fellowship from IBM Corp., through its Institutes of Innovation Program. J.T. was supported by Clinical Gene Networks AB and Link{\"o}ping University. T.R. was supported by National Institute of Mental Health Grant 2P30MH062261-07.",

year = "2008",

month = mar,

doi = "10.1016/j.ygeno.2007.11.005",

language = "English (US)",

volume = "91",

pages = "219--231",

journal = "Genomics",

issn = "0888-7543",

publisher = "Academic Press Inc.",

number = "3",

}

TY - JOUR

T1 - Integrated approaches to uncovering transcription regulatory networks in mammalian cells

AU - Tan, Kai

AU - Tegner, Jesper

AU - Ravasi, Timothy

N1 - Funding Information: K.T. was funded by a postdoctoral fellowship from IBM Corp., through its Institutes of Innovation Program. J.T. was supported by Clinical Gene Networks AB and Linköping University. T.R. was supported by National Institute of Mental Health Grant 2P30MH062261-07.

PY - 2008/3

Y1 - 2008/3

N2 - Integrative systems biology has emerged as an exciting research approach in molecular biology and functional genomics that involves the integration of genomics, proteomics, and metabolomics datasets. These endeavors establish a systematic paradigm by which to interrogate, model, and iteratively refine our knowledge of the regulatory events within a cell. Here we review the latest technologies available to collect high-throughput measurements of a cellular state as well as the most successful methods for the integration and interrogation of these measurements. In particular we will focus on methods available to infer transcription regulatory networks in mammals.

AB - Integrative systems biology has emerged as an exciting research approach in molecular biology and functional genomics that involves the integration of genomics, proteomics, and metabolomics datasets. These endeavors establish a systematic paradigm by which to interrogate, model, and iteratively refine our knowledge of the regulatory events within a cell. Here we review the latest technologies available to collect high-throughput measurements of a cellular state as well as the most successful methods for the integration and interrogation of these measurements. In particular we will focus on methods available to infer transcription regulatory networks in mammals.

KW - Bioinformatics

KW - Cellular networks

KW - ChIp-chip

KW - Dynamics

KW - Gene expression

KW - Gene networks

KW - Genomics

KW - Networks

KW - Personalized medicine

KW - Protein interaction maps

KW - Protein-protein interaction networks

KW - Systems biology

KW - Systems medicine

KW - Transcriptional networks

UR - http://www.scopus.com/inward/record.url?scp=39149109286&partnerID=8YFLogxK

U2 - 10.1016/j.ygeno.2007.11.005

DO - 10.1016/j.ygeno.2007.11.005

M3 - Review article

C2 - 18191937

AN - SCOPUS:39149109286

SN - 0888-7543

VL - 91

SP - 219

EP - 231

JO - Genomics

JF - Genomics

IS - 3

ER -

Integrated approaches to uncovering transcription regulatory networks in mammalian cells

Abstract

Keywords

ASJC Scopus subject areas

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