Data integration software tools | Mass spectrometry-based untargeted metabolomics
Metabolomics is a rapidly evolving field that holds promise to provide insights into genotype-phenotype relationships in cancers, diabetes and other complex diseases. One of the major informatics challenges is providing tools that link metabolite data with other types of high-throughput molecular data (e.g. transcriptomics, proteomics), and incorporate prior knowledge of pathways and molecular interactions.
A user-driven tool that displays large datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other processes. MapMan was developed for use with Arabidopsis, but has already been extended for use with several other species. These tools are available as downloadable and web-based versions.
Provides a web-based analytical pipeline for high-throughput metabolomics studies. MetaboAnalyst aims to offer a variety of commonly used procedures for metabolomic data processing, normalization, multivariate statistical analysis, as well as data annotation. The current implementation focuses on exploratory statistical analysis, functional interpretation, and advanced statistics for translational metabolomics studies. This tool is also available as desktop version.
Performs integrative analyses of two types of 'omics' variables that are measured on the same samples. integrOmics includes a regularized version of canonical correlation analysis to enlighten correlations between two datasets, and a sparse version of partial least squares (PLS) regression that includes simultaneous variable selection in both datasets.
A free open-source pathway analysis and drawing software. PathVisio allows you to draw, edit and analyse biological pathways. You can visualize your own experimental data on the pathways and find relevant pathways that are over-represented in your data set. PathVisio provides a basic set of features for pathway drawing, analysis and visualization. Additional features are available as plugins. Plugins are available for pathway building, pathway analysis, import/export functionality, data visualization or data integration. Plugins may be developed by anyone by using the PathVisio Plugin API.
Provides a bioinformatics framework for the visualization and interpretation of metabolomic and expression profiling data in the context of human metabolism. MetScape allows users to build and analyze networks of genes and compounds, identify enriched pathways from expression profiling data, and visualize changes in metabolite data. MetScape uses an internal relational database that integrates data from KEGG and EHMN.
Annotates metabolites in high precision mass spectrometry data. MassTRIX marks the identified chemical compounds on KEGG pathway maps using the KEGG/API. Selected genes or enzymes can be highlighted, e.g. to represent information on gene transcription or differences in the gene complement of different bacterial strains.
A statistical data analysis software that runs under Matlab enviroment. Though COVAIN was initially designed for metabolomics data processing, it can analyze other types of omics data, such as proteomics and transcriptomics. COVAIN gets its name from one of its functionalities: COVAriance INverse engineering. The design principle is to put most common data analysis methods – including preprocessing, uni- and multi-variate statistics, time-series analysis and network properties – into one software with a full graphical user interface (GUI) support, thus making data analysis more convenient for both biologists and bioinformatician.