Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae
Uncovering interactions between genes, gene networks, is important to increase our understanding of intrinsic cellular processes and responses to external stimuli such as drugs. Gene networks can be computationally inferred from repeated measurements of gene expression, using algorithms, which assum...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2008-01-01
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| Series: | Bioinformatics and Biology Insights |
| Subjects: | |
| Online Access: | http://la-press.com/article.php?article_id=909 |
| _version_ | 1818056744058748928 |
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| author | Jesper Lundström Johan Björkegren Jesper Tegnér |
| author_facet | Jesper Lundström Johan Björkegren Jesper Tegnér |
| author_sort | Jesper Lundström |
| collection | DOAJ |
| description | Uncovering interactions between genes, gene networks, is important to increase our understanding of intrinsic cellular processes and responses to external stimuli such as drugs. Gene networks can be computationally inferred from repeated measurements of gene expression, using algorithms, which assume that each gene is controlled by only a small number of other proteins. Here, by extending the transcription network with cofactors (defined from protein-protein binding data) as active regulators, we identified the effective gene network, providing evidence of in-hubs in the gene regulatory networks of yeast. Then, using the notion that in-hub genes will be differentially expressed over several experimental conditions, we designed an algorithm, the HubDetector, enabling identification of in-hubs directly from gene expression data. Applying the HubDetector to 488 genome-wide expression profiles from two independent datasets, we identified putative in-hubs overlapping significantly with in-hubs in the effective gene network. |
| first_indexed | 2024-12-10T12:33:42Z |
| format | Article |
| id | doaj.art-dab1904bd2004f82a2964fd0bbcf91c8 |
| institution | Directory Open Access Journal |
| issn | 1177-9322 |
| language | English |
| last_indexed | 2024-12-10T12:33:42Z |
| publishDate | 2008-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Bioinformatics and Biology Insights |
| spelling | doaj.art-dab1904bd2004f82a2964fd0bbcf91c82022-12-22T01:48:44ZengSAGE PublishingBioinformatics and Biology Insights1177-93222008-01-012313322Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces CerevisiaeJesper LundströmJohan BjörkegrenJesper TegnérUncovering interactions between genes, gene networks, is important to increase our understanding of intrinsic cellular processes and responses to external stimuli such as drugs. Gene networks can be computationally inferred from repeated measurements of gene expression, using algorithms, which assume that each gene is controlled by only a small number of other proteins. Here, by extending the transcription network with cofactors (defined from protein-protein binding data) as active regulators, we identified the effective gene network, providing evidence of in-hubs in the gene regulatory networks of yeast. Then, using the notion that in-hub genes will be differentially expressed over several experimental conditions, we designed an algorithm, the HubDetector, enabling identification of in-hubs directly from gene expression data. Applying the HubDetector to 488 genome-wide expression profiles from two independent datasets, we identified putative in-hubs overlapping significantly with in-hubs in the effective gene network.http://la-press.com/article.php?article_id=909gene expressionnetworkalgorithmtranscription regulationprotein-protein interactionsin-hubs |
| spellingShingle | Jesper Lundström Johan Björkegren Jesper Tegnér Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae Bioinformatics and Biology Insights gene expression network algorithm transcription regulation protein-protein interactions in-hubs |
| title | Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae |
| title_full | Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae |
| title_fullStr | Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae |
| title_full_unstemmed | Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae |
| title_short | Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae |
| title_sort | evidence of highly regulated genes in hubs in gene networks of saccharomyces cerevisiae |
| topic | gene expression network algorithm transcription regulation protein-protein interactions in-hubs |
| url | http://la-press.com/article.php?article_id=909 |
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