Table 1.
Tools for mapping metabolites into biochemical pathways
| Name | Description | Reference | URL |
|---|---|---|---|
| NA | Refine mass assignments through the intersection of peak correlation pairs with a database of biochemically relevant interaction pairs | Gipson et al. (2008) | NA |
| Metabolome Searcher | Simplify database search in MS databases by limiting the query to genome plausible metabolites | Dhanasekaran et al. (2015) | http://procyc.westcent.usu.edu/cgi-bin/MetaboSearcher.cgi |
| MassTRIX | Presents the MS identified chemical compounds in their genomic context as differentially coloured objects on KEGG pathway maps | Suhre and Schmitt-Kopplin (2008) | http://masstrix3.helmholtz-muenchen.de/masstrix3/ |
| MetaMapp | Map the detected metabolites in a MS experiment in a network graph | Barupal et al. (2012) | NA |
| MetExplore | To provide an interactive visualization of metabolic networks (or sub-networks) to mine metabolomics data | Cottret et al. (2010) | http://metexplore.toulouse.inra.fr/joomla3/index.php |
| Paintomics | Provide a simple but effective resource for integrated visualization in studies where transcriptomics and metabolomics data are generated on the same set of samples | García-Alcalde et al. (2011) | http://www.paintomics.org |
| KaPPa-View | A web-based tool for representing quantitative data for individual transcripts and/or metabolites on plant metabolic pathway maps | Tokimatsu et al. (2005) | http://kpv.kazusa.or.jp/ |
| MapMan | A user-driven tool that displays large data sets onto diagrams of metabolic pathways or other processes | Thimm et al. (2004) | http://mapman.gabipd.org/web/guest |
| ProMeTra | Visualizes and combines datasets from transcriptomics, proteomics, and metabolomics on user defined metabolic pathway maps, with the ability to generate enriched SVG images or animations via a user-friendly web interface | Neuweger et al. (2009) | https://omictools.com/prometra-tool |
| Metscape | Allows users to trace the connections between metabolites and genes, visualize compound networks and display compound structures as well as information for reactions, enzymes, genes, and pathways | Gao et al. (2010) | http://metscape.ncibi.org/ |