RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags
<p>Abstract</p> <p>Background</p> <p>Gene Regulatory Networks (GRNs) provide integrated views of gene interactions that control biological processes. Many public databases contain biological interactions extracted from experimentally validated literature reports, but mo...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2011-10-01
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| Series: | BMC Bioinformatics |
| _version_ | 1811266737959600128 |
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| author | Zhang Chaoyang Perkins Edward J Gong Ping Li Ying Wang Nan |
| author_facet | Zhang Chaoyang Perkins Edward J Gong Ping Li Ying Wang Nan |
| author_sort | Zhang Chaoyang |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Gene Regulatory Networks (GRNs) provide integrated views of gene interactions that control biological processes. Many public databases contain biological interactions extracted from experimentally validated literature reports, but most furnish only information for a few genetic model organisms. In order to provide a bioinformatic tool for researchers who work with non-model organisms, we developed RefNetBuilder, a new platform that allows construction of putative reference pathways or GRNs from expressed sequence tags (ESTs).</p> <p>Results</p> <p>RefNetBuilder was designed to have the flexibility to extract and archive pathway or GRN information from public databases such as the Kyoto Encyclopedia of Genes and Genomes (KEGG). It features sequence alignment tools such as BLAST to allow mapping ESTs to pathways and GRNs in model organisms. A scoring algorithm was incorporated to rank and select the best match for each query EST. We validated RefNetBuilder using DNA sequences of <it>Caenorhabditis elegans</it>, a model organism having manually curated KEGG pathways. Using the earthworm <it>Eisenia fetida</it> as an example, we demonstrated the functionalities and features of RefNetBuilder.</p> <p>Conclusions</p> <p>The RefNetBuilder provides a standalone application for building reference GRNs for non-model organisms on a number of operating system platforms with standard desktop computer hardware. As a new bioinformatic tool aimed for constructing putative GRNs for non-model organisms that have only ESTs available, RefNetBuilder is especially useful to explore pathway- or network-related information in these organisms.</p> |
| first_indexed | 2024-04-12T20:48:42Z |
| format | Article |
| id | doaj.art-ef4dd2537be24de29178d7a110542b30 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-12T20:48:42Z |
| publishDate | 2011-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-ef4dd2537be24de29178d7a110542b302022-12-22T03:17:12ZengBMCBMC Bioinformatics1471-21052011-10-0112Suppl 10S2010.1186/1471-2105-12-S10-S20RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tagsZhang ChaoyangPerkins Edward JGong PingLi YingWang Nan<p>Abstract</p> <p>Background</p> <p>Gene Regulatory Networks (GRNs) provide integrated views of gene interactions that control biological processes. Many public databases contain biological interactions extracted from experimentally validated literature reports, but most furnish only information for a few genetic model organisms. In order to provide a bioinformatic tool for researchers who work with non-model organisms, we developed RefNetBuilder, a new platform that allows construction of putative reference pathways or GRNs from expressed sequence tags (ESTs).</p> <p>Results</p> <p>RefNetBuilder was designed to have the flexibility to extract and archive pathway or GRN information from public databases such as the Kyoto Encyclopedia of Genes and Genomes (KEGG). It features sequence alignment tools such as BLAST to allow mapping ESTs to pathways and GRNs in model organisms. A scoring algorithm was incorporated to rank and select the best match for each query EST. We validated RefNetBuilder using DNA sequences of <it>Caenorhabditis elegans</it>, a model organism having manually curated KEGG pathways. Using the earthworm <it>Eisenia fetida</it> as an example, we demonstrated the functionalities and features of RefNetBuilder.</p> <p>Conclusions</p> <p>The RefNetBuilder provides a standalone application for building reference GRNs for non-model organisms on a number of operating system platforms with standard desktop computer hardware. As a new bioinformatic tool aimed for constructing putative GRNs for non-model organisms that have only ESTs available, RefNetBuilder is especially useful to explore pathway- or network-related information in these organisms.</p> |
| spellingShingle | Zhang Chaoyang Perkins Edward J Gong Ping Li Ying Wang Nan RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags BMC Bioinformatics |
| title | RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags |
| title_full | RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags |
| title_fullStr | RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags |
| title_full_unstemmed | RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags |
| title_short | RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags |
| title_sort | refnetbuilder a platform for construction of integrated reference gene regulatory networks from expressed sequence tags |
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