Table 1.
Biological databases and functional analysis tools
| Tools | Websites | References |
|---|---|---|
| Biological databases | ||
| KEGG (Kyoto Encyclopedia of Genes and Genomes) | http://www.genome.jp/kegg | (Kanehisa et al 2016) |
| HumanCyc (Encylopedia of Human Metabolic Pathways) | http://humancyc.org | (Romero et al 2005) |
| MetaCyc (Encyclopedia of Metabolic Pathways) | http://metacyc.org | (Caspi et al 2008) |
| Reactome (A Curated Knowledgebase of Pathways) | http://www.reactome.org | (Vastrik et al 2007) |
| SMPDB (Small Molecule Pathway Database) | http://www.smpdb.ca | (Jewison et al 2014) |
| Virtual Metabolic Human Database | https://vmh.uni.lu | (Thiele et al 2013) |
| Wikipathways | http://www.wikipathways.org | (Kelder et al 2012) |
| Pathway and networks analysis and visualization | ||
| BioCyc—Omics Viewer | http://biocyc.org | (Caspi et al 2016) |
| iPath | http://pathways.embl.de | (Yamada et al 2011) |
| MetScape | http://metscape.ncibi.org | (Karnovsky et al 2012) |
| Paintomics | http://www.paintomics.org | (Garcia-Alcalde et al 2011) |
| Pathos | http://motif.gla.ac.uk/Pathos | (Leader et al 2011) |
| Pathvisio | http://www.pathvisio.org | (Kutmon et al 2015) |
| VANTED | http://vanted.ipk-gatersleben.de | (Rohn et al 2012) |
| IMPaLA | http://impala.molgen.mpg.de | (Kamburov et al 2011) |
| MBROLE 2.0 | http://csbg.cnb.csic.es/mbrole2 | (Lopez-Ibanez et al 2016) |
| MPEA | http://ekhidna.biocenter.helsinki.fi/poxo/mpea | (Kankainen et al 2011) |
| Mummichog | http://clinicalmetabolomics.org/init/default/software | (Li et al 2013) |
| PIUMet | http://fraenkel-nsf.csbi.mit.edu/PIUMet/ | (Pirhaji et al 2016) |
| 3Omics | http://3omics.cmdm.tw/ | (Kuo et al 2013) |
| InCroMAP | http://www.ra.cs.uni-tuebingen.de/software/InCroMAP/ | (Wrzodek et al 2013) |
| Multifunctional tools | ||
| MetaboAnlayst | http://www.metaboanalyst.com | (Xia et al 2015) |
| XCMS online | https://xcmsonline.scripps.edu | (Tautenhahn et al 2012) |
| MASSyPup | http://www.bioprocess.org/massypup | (Winkler 2015) |
| Workflow4Metabolomics | http://workflow4metabolomics.org | (Giacomoni et al 2015) |
| Metabox | https://github.com/kwanjeeraw/metabox | (Wanichthanarak et al 2017) |