Journal
ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 31
Volume 31, Issue -, Pages 399-428Publisher
ANNUAL REVIEWS
DOI: 10.1146/annurev-cellbio-100913-012908
Keywords
gene regulatory networks; comparative functional genomics; evolution; cis-regulatory elements; coexpression modules; comparative sequencing; comparative expression; network analysis
Categories
Funding
- NATIONAL CANCER INSTITUTE [R01CA119176] Funding Source: NIH RePORTER
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [P50HG006193] Funding Source: NIH RePORTER
- Howard Hughes Medical Institute Funding Source: Medline
- NCI NIH HHS [R01CA119176-01] Funding Source: Medline
- NHGRI NIH HHS [P50HG006193] Funding Source: Medline
Ask authors/readers for more resources
Regulation of gene expression is central to many biological processes. Although reconstruction of regulatory circuits from genomic data alone is therefore desirable, this remains a major computational challenge. Comparative approaches that examine the conservation and divergence of circuits and their components across strains and species can help reconstruct circuits as well as provide insights into the evolution of gene regulatory processes and their adaptive contribution. In recent years, advances in genomic and computational tools have led to a wealth of methods for such analysis at the sequence, expression, pathway, module, and entire network level. Here, we review computational methods developed to study transcriptional regulatory networks using comparative genomics, from sequence to functional data. We highlight how these methods use evolutionary conservation and divergence to reliably detect regulatory components as well as estimate the extent and rate of divergence. Finally, we discuss the promise and open challenges in linking regulatory divergence to phenotypic divergence and adaptation.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available