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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Darnell, Cynthia L. Schmid, Amy K. |
| Description | Country affiliation: United States Author Affiliation: Darnell CL ( Biology Department, Duke University, Durham, NC 27708, USA.); Schmid AK ( Biology Department, Duke University, Durham, NC 27708, USA) |
| Abstract | To survive complex and changing environmental conditions, microorganisms use gene regulatory networks (GRNs) composed of interacting regulatory transcription factors (TFs) to control the timing and magnitude of gene expression. Genome-wide datasets; such as transcriptomics and protein-DNA interactions; and experiments such as high throughput growth curves; facilitate the construction of GRNs and provide insight into TF interactions occurring under stress. Systems biology approaches integrate these datasets into models of GRN architecture as well as statistical and/or dynamical models to understand the function of networks occurring in cells. Previously, these types of studies have focused on traditional model organisms (e.g. Escherichia coli, yeast). However, recent advances in archaeal genetics and other tools have enabled a systems approach to understanding GRNs in these relatively less studied archaeal model organisms. In this report, we outline a systems biology workflow for generating and integrating data focusing on the TF regulator. We discuss experimental design, outline the process of data collection, and provide the tools required to produce high confidence regulons for the TFs of interest. We provide a case study as an example of this workflow, describing the construction of a GRN centered on multi-TF coordinate control of gene expression governing the oxidative stress response in the hypersaline-adapted archaeon Halobacterium salinarum. |
| File Format | HTM / HTML |
| ISSN | 10462023 |
| Volume Number | 86 |
| e-ISSN | 10959130 |
| Journal | Methods |
| Language | English |
| Publisher | Elsevier |
| Publisher Date | 2015-09-15 |
| Publisher Place | United States |
| Access Restriction | One Nation One Subscription (ONOS) |
| Subject Keyword | Discipline Life sciences, Biochemistry Archaea Genetics Systems Biology Transcription Factors Transcription, Genetic Computational Biology Methods Gene Regulatory Networks Genome, Archaeal Halobacterium Salinarum Journal Article Research Support, U.s. Gov't, Non-p.h.s. |
| Content Type | Text |
| Resource Type | Article |
| Subject | Molecular Biology |
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