Computational Systems Biology Methods and Protocols.7z

study. They provide integrative metabolite information retrieving

from public databases, such as KEGG, SMPDB, HMDB, Pub-

Chem, and ChEBI. In short, these databases and tools can help

understand the biological roles of metabolites play in living systems.

7 Conclusions

Metabolomics is an important “omic” technology that can discover

clinic biomarker and provide deep mechanistic insights into

biological process for a living system. Here we review the experi-

mental design, sample collection and preparation methods, analyti-

cal platform of data acquisition (such as GC-MS, LC-MS, CE-MS,

NMR), the data preprocessing and analyzing methods, as well as

mechanism interpretation and hypothesis generation approaches

for metabolomics study. The challenges in metabolomics are the

Table 1
Software of mechanism interpretation for metabolites

Name URL Reference

MSEA http://www.msea.ca [122]

MBRole http://csbg.cnb.csic.es/mbrole [123]

MPEA http://ekhidna.biocenter.helsinki.fi/poxo/mpea/ [124]

IMPaLA http://impala.molgen.mpg.de [125]

KEGG http://www.genome.jp/kegg/pathway.html [126]

BioCyc—Omics

Viewer

http://biocyc.org [127]

iPath http://pathways.embl.de [128]

KaPPA-View http://kpv.kazusa.or.jp/en/ [129]

MapMan http://mapman.gabipd.org/web/guest/mapman [130]

MetPA http://metpa.metabolomics.ca [131]

Metscape http://metscape.ncibi.org [132]

MGV http://www.microarray-analysis.org/mayday [133]

Paintomics http://www.paintomics.org [134]

Pathos http://motif.gla.ac.uk/Pathos/ [135]

PathVisio http://www.pathvisio.org/[136]

ProMeTra http://www.cebitec.uni-bielefeld.de/groups/brf/software/

prometra_info/Reactome

[137]

Reactome http://www.reactome.org [138]

VANTED http://vanted.ipk-gatersleben.de [139]

284 Jing Cheng et al.