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. 2004 Jul 1;32(Web Server issue):W449-56.
doi: 10.1093/nar/gkh409.

Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments

Purvesh Khatri  1 , Pratik Bhavsar, Gagandeep Bawa, Sorin Draghici
Affiliations

Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments

Purvesh Khatri et al. Nucleic Acids Res. .

Abstract

The Onto-Tools suite is composed of an annotation database and five seamlessly integrated web-accessible data mining tools: Onto-Express (OE), Onto-Compare (OC), Onto-Design (OD), Onto-Translate (OT) and Onto-Miner (OM). OM is a new tool that provides a unified access point and an application programming interface for most annotations available. Our database has been enhanced with more than 120 new commercial microarrays and annotations for Rattus norvegicus, Drosophila melanogaster and Carnorhabditis elegans. The Onto-Tools have been redesigned to provide better biological insight, improved performance and user convenience. The new features implemented in OE include support for gene names, LocusLink IDs and Gene Ontology (GO) IDs, ability to specify fold changes for the input genes, links to the KEGG pathway database and detailed output files. OC allows comparisons of the functional bias of more than 170 commercial microarrays. The latest version of OD allows the user to specify keywords if the exact GO term is not known as well as providing more details than the previous version. OE, OC and OD now have an integrated GO browser that allows the user to customize the level of abstraction for each GO category. The Onto-Tools are available online at http://vortex.cs.wayne.edu/Projects.html.

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Figures

Figure 1
Figure 1
Onto-Tools integration (clockwise from top left). The user can analyze a set of differentially regulated genes using Onto-Express to find significantly affected biological processes. Onto-Compare can be used to find a suitable microarray for studying the hypotheses formulated based on these biological processes. If a suitable array is not found, Onto-Design can be used to design a custom array suitable for studying the hypotheses. One can refine the custom array design by creating the functional profile of the custom array and comparing it with the existing arrays. Once a suitable array is designed the user can either use Onto-Translate to obtain the list of GenBank accession numbers for the custom array or use Onto-Miner to obtain more details about each of the genes on the custom array such as the gene name, RefSeq accession number and chromosome location.
Figure 2
Figure 2
Integrated GO browser in Onto-Express (left) and Onto-Compare (right). The tree view in OE and OD allows the user to choose the desired level of abstraction for each GO category. The P-values for each term in OE are adjusted as the user chooses the desired level of abstraction for the term. The numbers of genes in each GO term for each array are modified appropriately as the terms are collapsed or expanded.
See this image and copyright information in PMC

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