TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements
<p>Abstract</p> <p>Background</p> <p>Transcription factors (TFs) regulate gene transcription and play pivotal roles in various biological processes such as development, cell cycle progression, cell differentiation and tumor suppression. Identifying <it>cis</it&...
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| Format: | Article |
| Language: | English |
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BMC
2007-11-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/8/441 |
| _version_ | 1811329466569326592 |
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| author | Brenner Sydney Yang Yuchen Lee Alison P Venkatesh Byrappa |
| author_facet | Brenner Sydney Yang Yuchen Lee Alison P Venkatesh Byrappa |
| author_sort | Brenner Sydney |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Transcription factors (TFs) regulate gene transcription and play pivotal roles in various biological processes such as development, cell cycle progression, cell differentiation and tumor suppression. Identifying <it>cis</it>-regulatory elements associated with TF-encoding genes is a crucial step in understanding gene regulatory networks. To this end, we have used a comparative genomics approach to identify putative <it>cis</it>-regulatory elements associated with TF-encoding genes in vertebrates.</p> <p>Description</p> <p>We have created a database named TFCONES (Transcription Factor Genes & Associated COnserved Noncoding ElementS) (<url>http://tfcones.fugu-sg.org</url>) which contains all human, mouse and fugu TF-encoding genes and conserved noncoding elements (CNEs) associated with them. The CNEs were identified by gene-by-gene alignments of orthologous TF-encoding gene loci using MLAGAN. We also predicted putative transcription factor binding sites within the CNEs. A significant proportion of human-fugu CNEs contain experimentally defined binding sites for transcriptional activators and repressors, indicating that a majority of the CNEs may function as transcriptional regulatory elements. The TF-encoding genes that are involved in nervous system development are generally enriched for human-fugu CNEs. Users can retrieve TF-encoding genes and their associated CNEs by conducting a keyword search or by selecting a family of DNA-binding proteins.</p> <p>Conclusion</p> <p>The conserved noncoding elements identified in TFCONES represent a catalog of highly prioritized putative <it>cis</it>-regulatory elements of TF-encoding genes and are candidates for functional assay.</p> |
| first_indexed | 2024-04-13T15:44:17Z |
| format | Article |
| id | doaj.art-898b40ef4a0e425cab6f31dbc306e967 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T15:44:17Z |
| publishDate | 2007-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-898b40ef4a0e425cab6f31dbc306e9672022-12-22T02:41:02ZengBMCBMC Genomics1471-21642007-11-018144110.1186/1471-2164-8-441TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elementsBrenner SydneyYang YuchenLee Alison PVenkatesh Byrappa<p>Abstract</p> <p>Background</p> <p>Transcription factors (TFs) regulate gene transcription and play pivotal roles in various biological processes such as development, cell cycle progression, cell differentiation and tumor suppression. Identifying <it>cis</it>-regulatory elements associated with TF-encoding genes is a crucial step in understanding gene regulatory networks. To this end, we have used a comparative genomics approach to identify putative <it>cis</it>-regulatory elements associated with TF-encoding genes in vertebrates.</p> <p>Description</p> <p>We have created a database named TFCONES (Transcription Factor Genes & Associated COnserved Noncoding ElementS) (<url>http://tfcones.fugu-sg.org</url>) which contains all human, mouse and fugu TF-encoding genes and conserved noncoding elements (CNEs) associated with them. The CNEs were identified by gene-by-gene alignments of orthologous TF-encoding gene loci using MLAGAN. We also predicted putative transcription factor binding sites within the CNEs. A significant proportion of human-fugu CNEs contain experimentally defined binding sites for transcriptional activators and repressors, indicating that a majority of the CNEs may function as transcriptional regulatory elements. The TF-encoding genes that are involved in nervous system development are generally enriched for human-fugu CNEs. Users can retrieve TF-encoding genes and their associated CNEs by conducting a keyword search or by selecting a family of DNA-binding proteins.</p> <p>Conclusion</p> <p>The conserved noncoding elements identified in TFCONES represent a catalog of highly prioritized putative <it>cis</it>-regulatory elements of TF-encoding genes and are candidates for functional assay.</p>http://www.biomedcentral.com/1471-2164/8/441 |
| spellingShingle | Brenner Sydney Yang Yuchen Lee Alison P Venkatesh Byrappa TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements BMC Genomics |
| title | TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements |
| title_full | TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements |
| title_fullStr | TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements |
| title_full_unstemmed | TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements |
| title_short | TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements |
| title_sort | tfcones a database of vertebrate transcription factor encoding genes and their associated conserved noncoding elements |
| url | http://www.biomedcentral.com/1471-2164/8/441 |
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