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GeneBins: a database for classifying gene expression data, with application to plant genome arrays.

Goffard N, Weiller G - BMC Bioinformatics (2007)

Bottom Line: The GeneBins database currently supports the functional classification of expression data from four Affymetrix arrays; Arabidopsis thaliana, Oryza sativa, Glycine max and Medicago truncatula.An online analysis tool to identify relevant functions is also provided.GeneBins provides resources to interpret gene expression results from microarray experiments.

View Article: PubMed Central - HTML - PubMed

Affiliation: ARC Centre of Excellence for Integrative Legume Research and Bioinformatics Laboratory, Genomic Interactions Group, Research School of Biological Sciences, Australian National University, Canberra, Australia. nicolas.goffard@anu.edu.au

ABSTRACT

Background: To interpret microarray experiments, several ontological analysis tools have been developed. However, current tools are limited to specific organisms.

Results: We developed a bioinformatics system to assign the probe set sequences of any organism to a hierarchical functional classification modelled on KEGG ontology. The GeneBins database currently supports the functional classification of expression data from four Affymetrix arrays; Arabidopsis thaliana, Oryza sativa, Glycine max and Medicago truncatula. An online analysis tool to identify relevant functions is also provided.

Conclusion: GeneBins provides resources to interpret gene expression results from microarray experiments. It is available at http://bioinfoserver.rsbs.anu.edu.au/utils/GeneBins/

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Screenshot of search results for the probe set Mtr.13998.1.S1_at in the Affymetrix Medicago Genome Array. This page shows: (a) information from the genome array, the database from which the sequence used to design this probe was taken, the accession number of a representative sequence and the associated description; (b) BIN assignment of the submitted probe set and its position in the hierarchy; (c) description and statistics of BLASTX best matches used to classify the probe set.
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Figure 1: Screenshot of search results for the probe set Mtr.13998.1.S1_at in the Affymetrix Medicago Genome Array. This page shows: (a) information from the genome array, the database from which the sequence used to design this probe was taken, the accession number of a representative sequence and the associated description; (b) BIN assignment of the submitted probe set and its position in the hierarchy; (c) description and statistics of BLASTX best matches used to classify the probe set.

Mentions: It is possible to retrieve the classification of a probe set in a selected genome array by its Affymetrix probe set identifier or by the GenBank accession number of the representative sequence. The results of database queries provide information on the probe set sequence, its position in the functional hierarchy, and the blast matches, as given in Figure 1. Note that a probe set can be assigned to more than one BIN. The cross-references associated to these BINs are displayed with a hyperlink to the entry in the corresponding database. The best BLAST matches are used to assign the probe set sequence to the BINs, provided that they exceed a pre-defined threshold E-value (10-8).


GeneBins: a database for classifying gene expression data, with application to plant genome arrays.

Goffard N, Weiller G - BMC Bioinformatics (2007)

Screenshot of search results for the probe set Mtr.13998.1.S1_at in the Affymetrix Medicago Genome Array. This page shows: (a) information from the genome array, the database from which the sequence used to design this probe was taken, the accession number of a representative sequence and the associated description; (b) BIN assignment of the submitted probe set and its position in the hierarchy; (c) description and statistics of BLASTX best matches used to classify the probe set.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1828068&req=5

Figure 1: Screenshot of search results for the probe set Mtr.13998.1.S1_at in the Affymetrix Medicago Genome Array. This page shows: (a) information from the genome array, the database from which the sequence used to design this probe was taken, the accession number of a representative sequence and the associated description; (b) BIN assignment of the submitted probe set and its position in the hierarchy; (c) description and statistics of BLASTX best matches used to classify the probe set.
Mentions: It is possible to retrieve the classification of a probe set in a selected genome array by its Affymetrix probe set identifier or by the GenBank accession number of the representative sequence. The results of database queries provide information on the probe set sequence, its position in the functional hierarchy, and the blast matches, as given in Figure 1. Note that a probe set can be assigned to more than one BIN. The cross-references associated to these BINs are displayed with a hyperlink to the entry in the corresponding database. The best BLAST matches are used to assign the probe set sequence to the BINs, provided that they exceed a pre-defined threshold E-value (10-8).

Bottom Line: The GeneBins database currently supports the functional classification of expression data from four Affymetrix arrays; Arabidopsis thaliana, Oryza sativa, Glycine max and Medicago truncatula.An online analysis tool to identify relevant functions is also provided.GeneBins provides resources to interpret gene expression results from microarray experiments.

View Article: PubMed Central - HTML - PubMed

Affiliation: ARC Centre of Excellence for Integrative Legume Research and Bioinformatics Laboratory, Genomic Interactions Group, Research School of Biological Sciences, Australian National University, Canberra, Australia. nicolas.goffard@anu.edu.au

ABSTRACT

Background: To interpret microarray experiments, several ontological analysis tools have been developed. However, current tools are limited to specific organisms.

Results: We developed a bioinformatics system to assign the probe set sequences of any organism to a hierarchical functional classification modelled on KEGG ontology. The GeneBins database currently supports the functional classification of expression data from four Affymetrix arrays; Arabidopsis thaliana, Oryza sativa, Glycine max and Medicago truncatula. An online analysis tool to identify relevant functions is also provided.

Conclusion: GeneBins provides resources to interpret gene expression results from microarray experiments. It is available at http://bioinfoserver.rsbs.anu.edu.au/utils/GeneBins/

Show MeSH