Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data
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 Transcripti...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2007-01-01
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| Series: | Bioinformatics and Biology Insights |
| Subjects: | |
| Online Access: | http://la-press.com/article.php?article_id=412 |
| _version_ | 1811285905397252096 |
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| author | Wei-Sheng Wu Bor-Sen Chen |
| author_facet | Wei-Sheng Wu Bor-Sen Chen |
| author_sort | Wei-Sheng Wu |
| collection | DOAJ |
| description | 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 bowtie 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. |
| first_indexed | 2024-04-13T02:51:48Z |
| format | Article |
| id | doaj.art-ef0ff0a7526043d18acc1b270679ab1e |
| institution | Directory Open Access Journal |
| issn | 1177-9322 |
| language | English |
| last_indexed | 2024-04-13T02:51:48Z |
| publishDate | 2007-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Bioinformatics and Biology Insights |
| spelling | doaj.art-ef0ff0a7526043d18acc1b270679ab1e2022-12-22T03:05:50ZengSAGE PublishingBioinformatics and Biology Insights1177-93222007-01-011917Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association DataWei-Sheng WuBor-Sen ChenUnicellular 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 bowtie 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.http://la-press.com/article.php?article_id=412stresstranscription factorgene expression data and TF-gene association data |
| spellingShingle | Wei-Sheng Wu Bor-Sen Chen Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data Bioinformatics and Biology Insights stress transcription factor gene expression data and TF-gene association data |
| title | Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data |
| title_full | Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data |
| title_fullStr | Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data |
| title_full_unstemmed | Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data |
| title_short | Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data |
| title_sort | identifying stress transcription factors using gene expression and tf gene association data |
| topic | stress transcription factor gene expression data and TF-gene association data |
| url | http://la-press.com/article.php?article_id=412 |
| work_keys_str_mv | AT weishengwu identifyingstresstranscriptionfactorsusinggeneexpressionandtfgeneassociationdata AT borsenchen identifyingstresstranscriptionfactorsusinggeneexpressionandtfgeneassociationdata |