SQUAT: A web tool to mine human, murine and avian SAGE data
<p>Abstract</p> <p>Background</p> <p>There is an increasing need in transcriptome research for gene expression data and pattern warehouses. It is of importance to integrate in these warehouses both raw transcriptomic data, as well as some properties encoded in these dat...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2008-09-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/9/378 |
| _version_ | 1818335020348080128 |
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| author | Besson Jérémy Boulicaut Jean-François Keime Céline Robardet Céline Blachon Sylvain Schicklin Stéphane Leyritz Johan Pensa Ruggero G Gandrillon Olivier |
| author_facet | Besson Jérémy Boulicaut Jean-François Keime Céline Robardet Céline Blachon Sylvain Schicklin Stéphane Leyritz Johan Pensa Ruggero G Gandrillon Olivier |
| author_sort | Besson Jérémy |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>There is an increasing need in transcriptome research for gene expression data and pattern warehouses. It is of importance to integrate in these warehouses both raw transcriptomic data, as well as some properties encoded in these data, like local patterns.</p> <p>Description</p> <p>We have developed an application called SQUAT (SAGE Querying and Analysis Tools) which is available at: <url>http://bsmc.insa-lyon.fr/squat/</url>. This database gives access to both raw SAGE data and patterns mined from these data, for three species (human, mouse and chicken). This database allows to make simple queries like "In which biological situations is my favorite gene expressed?" as well as much more complex queries like: ≪what are the genes that are frequently co-over-expressed with my gene of interest in given biological situations?≫. Connections with external web databases enrich biological interpretations, and enable sophisticated queries. To illustrate the power of SQUAT, we show and analyze the results of three different queries, one of which led to a biological hypothesis that was experimentally validated.</p> <p>Conclusion</p> <p>SQUAT is a user-friendly information retrieval platform, which aims at bringing some of the state-of-the-art mining tools to biologists.</p> |
| first_indexed | 2024-12-13T14:16:47Z |
| format | Article |
| id | doaj.art-325d3904916e42729c882c8f357d9629 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-13T14:16:47Z |
| publishDate | 2008-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-325d3904916e42729c882c8f357d96292022-12-21T23:42:16ZengBMCBMC Bioinformatics1471-21052008-09-019137810.1186/1471-2105-9-378SQUAT: A web tool to mine human, murine and avian SAGE dataBesson JérémyBoulicaut Jean-FrançoisKeime CélineRobardet CélineBlachon SylvainSchicklin StéphaneLeyritz JohanPensa Ruggero GGandrillon Olivier<p>Abstract</p> <p>Background</p> <p>There is an increasing need in transcriptome research for gene expression data and pattern warehouses. It is of importance to integrate in these warehouses both raw transcriptomic data, as well as some properties encoded in these data, like local patterns.</p> <p>Description</p> <p>We have developed an application called SQUAT (SAGE Querying and Analysis Tools) which is available at: <url>http://bsmc.insa-lyon.fr/squat/</url>. This database gives access to both raw SAGE data and patterns mined from these data, for three species (human, mouse and chicken). This database allows to make simple queries like "In which biological situations is my favorite gene expressed?" as well as much more complex queries like: ≪what are the genes that are frequently co-over-expressed with my gene of interest in given biological situations?≫. Connections with external web databases enrich biological interpretations, and enable sophisticated queries. To illustrate the power of SQUAT, we show and analyze the results of three different queries, one of which led to a biological hypothesis that was experimentally validated.</p> <p>Conclusion</p> <p>SQUAT is a user-friendly information retrieval platform, which aims at bringing some of the state-of-the-art mining tools to biologists.</p>http://www.biomedcentral.com/1471-2105/9/378 |
| spellingShingle | Besson Jérémy Boulicaut Jean-François Keime Céline Robardet Céline Blachon Sylvain Schicklin Stéphane Leyritz Johan Pensa Ruggero G Gandrillon Olivier SQUAT: A web tool to mine human, murine and avian SAGE data BMC Bioinformatics |
| title | SQUAT: A web tool to mine human, murine and avian SAGE data |
| title_full | SQUAT: A web tool to mine human, murine and avian SAGE data |
| title_fullStr | SQUAT: A web tool to mine human, murine and avian SAGE data |
| title_full_unstemmed | SQUAT: A web tool to mine human, murine and avian SAGE data |
| title_short | SQUAT: A web tool to mine human, murine and avian SAGE data |
| title_sort | squat a web tool to mine human murine and avian sage data |
| url | http://www.biomedcentral.com/1471-2105/9/378 |
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