Biomaterial Database

Computational approaches to the integration of gene expression, ChIP-chip and sequence data in the inference of gene regulatory networks. 2009

Emma J Cooke, and Richard S Savage, and David L Wild

MOAC Doctoral Training Centre, University of Warwick, Coventry CV4 7AL, UK.

A major challenge in systems biology is the ability to model complex regulatory interactions, such as gene regulatory networks, and a number of computational approaches have been developed over recent years to address this challenge. This paper reviews a number of these approaches, with a focus on probabilistic graphical models and the integration of diverse data sets, such as gene expression and transcription factor binding site location and activity.

UI	MeSH Term	Description	Entries
D015870	Gene Expression	The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.	Expression, Gene,Expressions, Gene,Gene Expressions
D017422	Sequence Analysis, DNA	A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.	DNA Sequence Analysis,Sequence Determination, DNA,Analysis, DNA Sequence,DNA Sequence Determination,DNA Sequence Determinations,DNA Sequencing,Determination, DNA Sequence,Determinations, DNA Sequence,Sequence Determinations, DNA,Analyses, DNA Sequence,DNA Sequence Analyses,Sequence Analyses, DNA,Sequencing, DNA
D047369	Chromatin Immunoprecipitation	A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.	Immunoprecipitation, Chromatin
D049490	Systems Biology	Comprehensive, methodical analysis of complex biological systems by monitoring responses to perturbations of biological processes. Large scale, computerized collection and analysis of the data are used to develop and test models of biological systems.	Biology, Systems
D053263	Gene Regulatory Networks	Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.	Gene Circuits,Gene Modules,Gene Networks,Transcriptional Networks,Gene Module,Circuit, Gene,Circuits, Gene,Gene Circuit,Gene Network,Gene Regulatory Network,Module, Gene,Modules, Gene,Network, Gene,Network, Gene Regulatory,Network, Transcriptional,Networks, Gene,Networks, Gene Regulatory,Networks, Transcriptional,Regulatory Network, Gene,Regulatory Networks, Gene,Transcriptional Network
D020411	Oligonucleotide Array Sequence Analysis	Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.	DNA Microarrays,Gene Expression Microarray Analysis,Oligonucleotide Arrays,cDNA Microarrays,DNA Arrays,DNA Chips,DNA Microchips,Gene Chips,Oligodeoxyribonucleotide Array Sequence Analysis,Oligonucleotide Microarrays,Sequence Analysis, Oligonucleotide Array,cDNA Arrays,Array, DNA,Array, Oligonucleotide,Array, cDNA,Arrays, DNA,Arrays, Oligonucleotide,Arrays, cDNA,Chip, DNA,Chip, Gene,Chips, DNA,Chips, Gene,DNA Array,DNA Chip,DNA Microarray,DNA Microchip,Gene Chip,Microarray, DNA,Microarray, Oligonucleotide,Microarray, cDNA,Microarrays, DNA,Microarrays, Oligonucleotide,Microarrays, cDNA,Microchip, DNA,Microchips, DNA,Oligonucleotide Array,Oligonucleotide Microarray,cDNA Array,cDNA Microarray