New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate

Abstract

The Onto-Tools suite is composed of an annotation database and eight complementary, web-accessible data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express and nsSNPCounter. Promoter-Express is a new tool added to the Onto-Tools ensemble that facilitates the identification of transcription factor binding sites active in specific conditions. nsSNPCounter is another new tool that allows computation and analysis of synonymous and non-synonymous codon substitutions for studying evolutionary rates of protein coding genes. Onto-Translate has also been enhanced to expand its scope and accuracy by fully utilizing the capabilities of the Onto-Tools database. Currently, Onto-Translate allows arbitrary mappings between 28 types of IDs for 53 organisms. Onto-Tools are freely available at .

Insights into novel cellular injury mechanisms by gene expression profiling in nephropathic cystinosis

“…Cluster and TreeView programs (Eisen et al 1998) were used to generate and visualize the hierarchical clusters of the samples, measuring similarity of gene expression and across arrays. Three approaches were used to assess the functional composition of genes assessed as significantly associated with cystinosis phenotype: Ingenuity Pathway Analysis (IPA) was used to identify the functional networks, canonical pathways, and involved functions and diseases; Gene ontology (GO) (http://www.geneontology.org/) was used to identify the relevant biological progress, cellular component, and molecular functions; and Pathway Express (Khatri et al 2006) was used to identify genes associated with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Either hypergeometric gene enrichment scores or an FDR are reported for each functional category in these tools.…”

IdMapper: A Java Application for ID Mapping across Multiple Cross-referencing Providers

“…A small research group can not afford its own mapping service and relies on external services. There exist efforts to reconcile identifiers across multiple source databases, such as the David gene ID conversion tool (Huang et al, 2008), MatchMiner (Bussey et al, 2003), IDconverter (Alibes et al, 2007), Onto-translate (Khatri et al, 2006), PICR (Cote et al, 2007), Synergizer (Brriz et al, 2008), and Biomart (Smedley et al, 2009).…”

Onto-Tools: new additions and improvements in 2006

“…(2,5,7,8); (v) Onto-Miner—provides a unified access point and an application programming interface (API) allowing queries for various information such as the gene name, official symbol, reference accession number, coded protein, etc. (4); (vi) Promoter-Express—which allows the users to find condition-specific transcription factor binding sites (TFBSs) (7,9) and (vii) nsSNPCounter—which allows analysis of synonymous and non-synonymous codon substitutions in protein coding genes (7). Previous publications have described in detail the motivation, implementation and validation of these tools.…”