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. 2005 Jul 1;33(Web Server issue):W762-5.
doi: 10.1093/nar/gki472.

Recent additions and improvements to the Onto-Tools

Purvesh Khatri  1 , Sivakumar Sellamuthu, Pooja Malhotra, Kashyap Amin, Arina Done, Sorin Draghici
Affiliations

Recent additions and improvements to the Onto-Tools

Purvesh Khatri et al. Nucleic Acids Res. .

Abstract

The Onto-Tools suite is composed of an annotation database and six seamlessly integrated, web-accessible data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner and Pathway-Express. The Onto-Tools database has been expanded to include various types of data from 12 new databases. Our database now integrates different types of genomic data from 19 sequence, gene, protein and annotation databases. Additionally, our database is also expanded to include complete Gene Ontology (GO) annotations. Using the enhanced database and GO annotations, Onto-Express now allows functional profiling for 24 organisms and supports 17 different types of input IDs. Onto-Translate is also enhanced to fully utilize the capabilities of the new Onto-Tools database with an ultimate goal of providing the users with a non-redundant and complete mapping from any type of identification system to any other type. Currently, Onto-Translate allows arbitrary mappings between 29 types of IDs. Pathway-Express is a new tool that helps the users find the most interesting pathways for their input list of genes. Onto-Tools are freely available at http://vortex.cs.wayne.edu/Projects.html.

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Figures

Figure 1
Figure 1
Pathway-Express (PE) performs a pathway level impact analysis and orders the affected pathways in the decreasing order of their expected importance for the given condition (panel 1). PE displays details about each pathway including: the source database, the total number of genes, etc. (panel 2). Panel 3 shows the gene symbols, expression values (or fold changes), and gene names for the differentially regulated genes. Panel 4 contains details about each pathway, including all genes in the pathway with their perturbation factors and expression levels. The users can also visualize the input genes in a pathway diagram. The input genes are highlighted in red color on the pathway diagram (panel 5).
See this image and copyright information in PMC

References

    1. Draghici S., Khatri P., Martins R.P., Ostermeier G.C., Krawetz S.A. Global functional profiling of gene expression. Genomics. 2003;81:98–104. - PubMed
    1. Draghici S., Khatri P., Shah A., Tainsky M. Assessing the functional bias of commercial microarrays using the Onto-Compare database. Biotechniques. 2003;(Suppl.):55–61. - PubMed
    1. Drăghici S., Khatri P., Bhavsar P., Shah A., Krawetz S.A., Tainsky M.A. Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res. 2003;31:3775–3781. - PMC - PubMed
    1. Khatri P., Bhavsar P., Bawa G., Drăghici S. Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. Nucleic Acids Res. 2004;32:W449–W556. - PMC - PubMed
    1. Khatri P., Drăghici S., Ostermeier G.C., Krawetz S.A. Profiling gene expression with Onto-Express. Genomics. 2002;79:266–270. - PubMed

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