Chemical enrichment analysis software tools | Drug discovery data analysis
Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis.
Performs overrepresentation (enrichment) analysis of categorical annotations for a set of compounds of interest. These categorical annotations correspond to biological and chemical information available in a number of public databases and software. Although focused on qualitative annotations, MBRole is general and versatile enough to perform functional enrichment analysis in any metabolomic sample (including additional biological and chemical annotations for human metabolites), and hence complements existing software for the rising field of metabolomics.
A rapid tool for functional analysis and biological interpretation of metabolic profiling data. MPEA follows the concept of gene set enrichment analysis (GSEA) and tests whether metabolites involved in some predefined pathway occur towards the top (or bottom) of a ranked query compound list. In particular, MPEA is designed to handle many-to-many relationships that may occur between the query compounds and metabolite annotations.
An enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology. BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.
A chemical annotation retrieval toolkit. As a key functionality, CART matches an input list of chemical names into a comprehensive reference space to assign unambiguous chemical identifiers. In this unified space, bioactivity annotations can be easily retrieved from databases covering a wide variety of chemical effects on biological systems. Subsequently, CART can determine annotations enriched in the input set of chemicals and display these in tabular format and interactive network visualizations, thereby facilitating integrative analysis of chemical bioactivity data.
Builds chemical and biological annotations for Tox21 assay data. Tox21 Enricher significantly recognizes over-represented chemical/biological annotations among sets of chemicals. It employs a modified Fisher’s exact test to proceed. This tool can be used for the evaluation of the significance of annotation enrichment. It furnishes a solution to improve the understanding of common chemical and toxicological properties.