Document Detail


Predictive modeling of genome-wide mRNA expression: from modules to molecules.
MedLine Citation:
PMID:  17311525     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Various algorithms are available for predicting mRNA expression and modeling gene regulatory processes. They differ in whether they rely on the existence of modules of coregulated genes or build a model that applies to all genes, whether they represent regulatory activities as hidden variables or as mRNA levels, and whether they implicitly or explicitly model the complex cis-regulatory logic of multiple interacting transcription factors binding the same DNA. The fact that functional genomics data of different types reflect the same molecular processes provides a natural strategy for integrative computational analysis. One promising avenue toward an accurate and comprehensive model of gene regulation combines biophysical modeling of the interactions among proteins, DNA, and RNA with the use of large-scale functional genomics data to estimate regulatory network connectivity and activity parameters. As the ability of these models to represent complex cis-regulatory logic increases, the need for approaches based on cross-species conservation may diminish.
Authors:
Harmen J Bussemaker; Barrett C Foat; Lucas D Ward
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Review    
Journal Detail:
Title:  Annual review of biophysics and biomolecular structure     Volume:  36     ISSN:  1056-8700     ISO Abbreviation:  Annu Rev Biophys Biomol Struct     Publication Date:  2007  
Date Detail:
Created Date:  2007-05-04     Completed Date:  2007-08-09     Revised Date:  2013-04-11    
Medline Journal Info:
Nlm Unique ID:  9211097     Medline TA:  Annu Rev Biophys Biomol Struct     Country:  United States    
Other Details:
Languages:  eng     Pagination:  329-47     Citation Subset:  IM    
Affiliation:
Department of Biological Sciences, Columbia University, New York, New York 10027, USA. hjb2004@columbia.edu
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MeSH Terms
Descriptor/Qualifier:
Algorithms
Animals
Base Sequence
Gene Expression Profiling
Gene Expression Regulation*
Genome*
Humans
Macromolecular Substances
Models, Theoretical
Molecular Conformation
Molecular Sequence Data
RNA Processing, Post-Transcriptional
RNA, Messenger / metabolism*
Transcription Factors / metabolism
Transcription, Genetic
Grant Support
ID/Acronym/Agency:
R01 HG003008/HG/NHGRI NIH HHS; R01HG003008/HG/NHGRI NIH HHS; R24GM074105/GM/NIGMS NIH HHS; U54CA121852/CA/NCI NIH HHS
Chemical
Reg. No./Substance:
0/Macromolecular Substances; 0/RNA, Messenger; 0/Transcription Factors

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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