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The Medicago truncatula gene expression atlas web server
BACKGROUND: Legumes (Leguminosae or Fabaceae) play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of legume genes. With the rapid growth of publically available Affymetrix GeneC...
Autores principales: | , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2804685/ https://www.ncbi.nlm.nih.gov/pubmed/20028527 http://dx.doi.org/10.1186/1471-2105-10-441 |
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author | He, Ji Benedito, Vagner A Wang, Mingyi Murray, Jeremy D Zhao, Patrick X Tang, Yuhong Udvardi, Michael K |
author_facet | He, Ji Benedito, Vagner A Wang, Mingyi Murray, Jeremy D Zhao, Patrick X Tang, Yuhong Udvardi, Michael K |
author_sort | He, Ji |
collection | PubMed |
description | BACKGROUND: Legumes (Leguminosae or Fabaceae) play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of legume genes. With the rapid growth of publically available Affymetrix GeneChip Medicago Genome Array GeneChip data from a great range of tissues, cell types, growth conditions, and stress treatments, the legume research community desires an effective bioinformatics system to aid efforts to interpret the Medicago genome through functional genomics. We developed the Medicago truncatula Gene Expression Atlas (MtGEA) web server for this purpose. DESCRIPTION: The Medicago truncatula Gene Expression Atlas (MtGEA) web server is a centralized platform for analyzing the Medicago transcriptome. Currently, the web server hosts gene expression data from 156 Affymetrix GeneChip(® )Medicago genome arrays in 64 different experiments, covering a broad range of developmental and environmental conditions. The server enables flexible, multifaceted analyses of transcript data and provides a range of additional information about genes, including different types of annotation and links to the genome sequence, which help users formulate hypotheses about gene function. Transcript data can be accessed using Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, GO and KEGG annotation terms, and InterPro domain number. Transcripts can also be discovered through co-expression or differential expression analysis. Flexible tools to select a subset of experiments and to visualize and compare expression profiles of multiple genes have been implemented. Data can be downloaded, in part or full, in a tabular form compatible with common analytical and visualization software. The web server will be updated on a regular basis to incorporate new gene expression data and genome annotation, and is accessible at: http://bioinfo.noble.org/gene-atlas/. CONCLUSIONS: The MtGEA web server has a well managed rich data set, and offers data retrieval and analysis tools provided in the web platform. It's proven to be a powerful resource for plant biologists to effectively and efficiently identify Medicago transcripts of interest from a multitude of aspects, formulate hypothesis about gene function, and overall interpret the Medicago genome from a systematic point of view. |
format | Text |
id | pubmed-2804685 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-28046852010-01-12 The Medicago truncatula gene expression atlas web server He, Ji Benedito, Vagner A Wang, Mingyi Murray, Jeremy D Zhao, Patrick X Tang, Yuhong Udvardi, Michael K BMC Bioinformatics Database BACKGROUND: Legumes (Leguminosae or Fabaceae) play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of legume genes. With the rapid growth of publically available Affymetrix GeneChip Medicago Genome Array GeneChip data from a great range of tissues, cell types, growth conditions, and stress treatments, the legume research community desires an effective bioinformatics system to aid efforts to interpret the Medicago genome through functional genomics. We developed the Medicago truncatula Gene Expression Atlas (MtGEA) web server for this purpose. DESCRIPTION: The Medicago truncatula Gene Expression Atlas (MtGEA) web server is a centralized platform for analyzing the Medicago transcriptome. Currently, the web server hosts gene expression data from 156 Affymetrix GeneChip(® )Medicago genome arrays in 64 different experiments, covering a broad range of developmental and environmental conditions. The server enables flexible, multifaceted analyses of transcript data and provides a range of additional information about genes, including different types of annotation and links to the genome sequence, which help users formulate hypotheses about gene function. Transcript data can be accessed using Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, GO and KEGG annotation terms, and InterPro domain number. Transcripts can also be discovered through co-expression or differential expression analysis. Flexible tools to select a subset of experiments and to visualize and compare expression profiles of multiple genes have been implemented. Data can be downloaded, in part or full, in a tabular form compatible with common analytical and visualization software. The web server will be updated on a regular basis to incorporate new gene expression data and genome annotation, and is accessible at: http://bioinfo.noble.org/gene-atlas/. CONCLUSIONS: The MtGEA web server has a well managed rich data set, and offers data retrieval and analysis tools provided in the web platform. It's proven to be a powerful resource for plant biologists to effectively and efficiently identify Medicago transcripts of interest from a multitude of aspects, formulate hypothesis about gene function, and overall interpret the Medicago genome from a systematic point of view. BioMed Central 2009-12-22 /pmc/articles/PMC2804685/ /pubmed/20028527 http://dx.doi.org/10.1186/1471-2105-10-441 Text en Copyright ©2009 He et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Database He, Ji Benedito, Vagner A Wang, Mingyi Murray, Jeremy D Zhao, Patrick X Tang, Yuhong Udvardi, Michael K The Medicago truncatula gene expression atlas web server |
title | The Medicago truncatula gene expression atlas web server |
title_full | The Medicago truncatula gene expression atlas web server |
title_fullStr | The Medicago truncatula gene expression atlas web server |
title_full_unstemmed | The Medicago truncatula gene expression atlas web server |
title_short | The Medicago truncatula gene expression atlas web server |
title_sort | medicago truncatula gene expression atlas web server |
topic | Database |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2804685/ https://www.ncbi.nlm.nih.gov/pubmed/20028527 http://dx.doi.org/10.1186/1471-2105-10-441 |
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