Onto-Tools: new additions and improvements in 2006

Abstract

Onto-Tools is a freely available web-accessible software suite, composed of an annotation database and nine complementary data-mining tools. This article describes a new tool, Onto-Express-to-go (OE2GO), as well as some new features implemented in Pathway-Express and Onto-Miner over the past year. Pathway-Express (PE) has been enhanced to identify significantly perturbed pathways in a given condition using the differentially expressed genes in the input. OE2GO is a tool for functional profiling using custom annotations. The development of this tool was aimed at the researchers working with organisms for which annotations are not yet available in the public domain. OE2GO allows researchers to use either annotation data from the Onto-Tools database, or their own custom annotations. By removing the necessity to use any specific database, OE2GO makes the functional profiling available for all organisms, with annotations using any ontology. The Onto-Tools are freely available at http://vortex.cs.wayne.edu/projects.htm.

TACC3-TSC2 maintains nuclear envelope structure and controls cell division

“…53 Comparisons were made for all possible microarray probe pairs and p values adjusted for multiple testing using the Bonferroni approach. Enrichment in GO term annotations was computed using the Onto-Express tool 93 with all coding human genes as reference. The GSEA 73 was run using the Gene Expression Omnibus reference GSE5923, 72 with default values for all the parameters except for the median probe instead of the max probe as the collapse method when multiple probe sets map to the same gene.…”

Gene expression profiling integrated into network modelling reveals heterogeneity in the mechanisms of BRCA1 tumorigenesis

“…Differentially expressed genes were declared after applying a twotail t-test with the P-values adjusted for the false discovery rate (FDR) using the Tibshirani and Efron approach (Tibshirani and Efron, 2002). Representation of Gene Ontology (GO) terms was examined using the Onto-Express tool (Khatri et al, 2007), with the reference including all genes in the array that passed quality filters and with P-values calculated based on the hypergeometric distribution and corrected using the FDR approach. Unsupervised clustering was performed in the R programming language (82) using the Euclidean distance and Ward's minimum variance method, except in the analysis of basal markers, which was performed with the correlation and average-linkage clustering method.…”

“…Shortest distances were calculated using only the giant network component and the geodesic formulation given by Freeman (Stelzl et al, 2005) using the R programming language (82). Differences between distributions of shortest paths were assessed with the Mann -Whitney U-test and GO term representations evaluated with the Onto-Express tool (Khatri et al, 2007), taking as a reference the protein set of the giant network component.…”

Global Gene Expression Analysis Identifies PDEF Transcriptional Networks Regulating Cell Migration during Cancer Progression

“…A differential expression cut-off of 1.5-fold was used to filter differentially expressed genes resulting from PDEF expression in the invasive cell lines. Gene ontology classification was performed using Pathway-Express by using the default parameters (Khatri et al, 2005;Draghici et al, 2007;Khatri et al, 2007).…”

“…To isolate putative PDEF regulatory target genes that are associated with cell migration, gene ontology associations were examined using Pathway Express (PE) (Khatri et al, 2005;Draghici et al, 2007;Khatri et al, 2007), a freely available web based tool (http://vortex.cs.wayne.edu). PE associates lists of genes with biological interaction pathways and provides an assessment of the impact that those genes have on the pathway of interest.…”