Onto-Express

[…] on for various types of data (functional, regulatory, and structural) by searching for frequent patterns among annotations and evaluating statistical relevance . This new approach, superior to DAVID, Onto‐Express, ProfCom or FATIGO+ by overcoming the lack of term–term relationships in these analyses, profiles different sides of the same information and offers a more accurate interpretation of the […]

[…] sing a threshold of >2-fold changes in expression. P < 0.05 was considered statistically significant. The analysis of biological processes affected by Thy1 in lung, myofibroblasts was performed using Onto-Express software (Open Channel Foundation, Chicago, IL, USA). […]

[…] sis. The hierarchical clustering was performed using CLUSTER and TREEVIEW program (M.B. Eisen, http://rana.lbl.gov). We considered 1.5 fold of expression change as baseline of up- or down-regulation. OntoExpress program was applied for ontological analysis,[] and cytoscape program was applied for interaction network analysis[] in which databases of BOND (http://bond.unleashedinformatics.com) and t […]

[…] arrays of one group (wt or RGS9-deficient mice) . Statistical testing was done using a two-tailed Student’s t-test. For gene ontology profiling, MAS5 normalized data with P≤0.01 were subjected to the Onto Express algorithm –. The settings were: hypergeometric distribution, correction for false discovery rate (fdr). The MAS5 processed data were also analyzed using the Gene Set Enrichment Analysis ( […]

[…] differentially expressed genes, lesser expressed genes were filtered out at a cutoff level of FC > 1.5, producing a list of the 130 most differentially expressed genes. This dataset was imported into Onto-Express and Pathway Express [,], part of the Onto-Tools software suite, for functional analysis, and grouped into Gene Ontology (GO) terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) cellu […]

[…] α1=0.01, α2=0.01, λ1=0, λ2=0.01, t1=1, and t2=1. Next, we obtain 81, 37, and 448 genes for the three factors, respectively. As in [], we then performed gene set enrichment analysis (GSEA) by applying Onto-Express [] on each of these sets of genes. Part of the result is shown in Table . We can see that the factor-specific genes selected by NMF correspond to some biological processes significantly. […]