GAM: a web-service for integrated transcriptional and metabolic network analysis.
Novel techniques for high-throughput steady-state metabolomic profiling yield information about changes of nearly thousands of metabolites. Such metabolomic profiles, when analyzed together with transcriptional profiles, can reveal novel insights about underlying biological processes. While a number of conceptual approaches have been developed for data integration, easily accessible tools for integrated analysis of mammalian steady-state metabolomic and transcriptional data are lacking. Here we present GAM ('genes and metabolites'): a web-service for integrated network analysis of transcriptional and steady-state metabolomic data focused on identification of the most changing metabolic subnetworks between two conditions of interest. In the web-service, we have pre-assembled metabolic networks for humans, mice, Arabidopsis and yeast and adapted exact solvers for an optimal subgraph search to work in the context of these metabolic networks. The output is the most regulated metabolic subnetwork of size controlled by false discovery rate parameters. The subnetworks are then visualized online and also can be downloaded in Cytoscape format for subsequent processing. The web-service is available at: https://artyomovlab.wustl.edu/shiny/gam/.
Computer Technologies Department, ITMO University, Saint Petersburg, 197101, Russia Department of Pathology & Immunology, Washington University in St. Louis, St.Louis, MO 63110, USA alsergbox@gmail.com.
Alexey A
0000-0003-1159-7220
AA
Sergushichev
Computer Technologies Department, ITMO University, Saint Petersburg, 197101, Russia.
Alexander A
AA
Loboda
Agios Pharmaceuticals, Cambridge, MA 02139, USA.
Abhishek K
AK
Jha
Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada.
Emma E
EE
Vincent
General Metabolics, Winchester, MA 01890, USA.
Edward M
EM
Driggers
Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada.
Russell G
RG
Jones
Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, D-79108, Germany.
Edward J
EJ
Pearce
Computer Technologies Department, ITMO University, Saint Petersburg, 197101, Russia Department of Pathology & Immunology, Washington University in St. Louis, St.Louis, MO 63110, USA martyomov@pathology.wustl.edu.
Maxim N
MN
Artyomov
D000465:Algorithms; D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D045744:Cell Line, Tumor; D003196:Computer Graphics; D030541:Databases, Genetic; D004847:Epithelial Cells / Q000378:metabolism / Q000473:pathology; D006801:Humans; D020407:Internet; D008262:Macrophage Activation / Q000235:genetics / Q000276:immunology; D008264:Macrophages / Q000166:cytology / Q000276:immunology / Q000378:metabolism; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D055442:Metabolome / Q000235:genetics*; D051379:Mice; D061251:Primary Cell Culture; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012984:Software; D013045:Species Specificity; D014158:Transcription, Genetic