ArticleBioinformatics and biology insights2009
Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data.
Article in Bioinformatics and biology insights, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 17 citations in OpenAlex.
- Decoding nitrogen uptake efficiency in maize and sorghum: insights from comparative gene regulatory networks.The Plant journal : for cell and molecular biology · 2025Article
- Global gene expression profiling under nitrogen stress identifies key genes involved in nitrogen stress adaptation in maize (Zea mays L.).Scientific reports · 2022Article
- Stress tolerance enhancement via SPT15 base editing in Saccharomyces cerevisiae.Biotechnology for biofuels · 2021Article
- A Hierarchical Transcriptional Regulatory Network Required for Long-Term Thermal Stress Tolerance in an IndustrialFrontiers in bioengineering and biotechnology · 2021Article
- MIG1 as a positive regulator for the histidine biosynthesis pathway and as a global regulator in thermotolerant yeast Kluyveromyces marxianus.Scientific reports · 2019Article
- Characterizing building blocks of resource constrained biological networks.BMC bioinformatics · 2019Article
- Morphological and Transcriptome Analysis of Wheat Seedlings Response to Low Nitrogen Stress.Plants (Basel, Switzerland) · 2019Article
- Cross-stress resistance in Saccharomyces cerevisiae yeast--new insight into an old phenomenon.Cell stress & chaperones · 2016Review
- Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast.Molecular systems biology · 2013Article
- Systematic identification of yeast cell cycle transcription factors using multiple data sources.BMC bioinformatics · 2008Article
- Identifying gene regulatory modules of heat shock response in yeast.BMC genomics · 2008Article
- Reconstructing a network of stress-response regulators via dynamic system modeling of gene regulation.Gene regulation and systems biology · 2008Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Unicellular organisms such as yeasts have evolved to survive environmental stresses by rapidly reorganizing the genomic expression program to meet the challenges of harsh environments. The complex adaptation mechanisms to stress remain to be elucidated. In this study, we developed Stress Transcription Factor Identification Algorithm (STFIA), which integrates gene expression and TF-gene association data to identify the stress transcription factors (TFs) of six kinds of stresses. We identified some general stress TFs that are in response to various stresses, and some specific stress TFs that are in response to one specific stress. The biological significance of our findings is validated by the literature. We found that a small number of TFs may be sufficient to control a wide variety of expression patterns in yeast under different stresses. Two implications can be inferred from this observation. First, the adaptation mechanisms to different stresses may have a bow-tie structure. Second, there may exist extensive regulatory cross-talk among different stress responses. In conclusion, this study proposes a network of the regulators of stress responses and their mechanism of action.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.