DATABASESThe human gut microbiota produces diverse, extensive metabolites that have the potential to affect host physiology. Despite significant efforts to identify metabolic pathways for producing these microbial metabolites, a comprehensive metabolic pathway database for the human gut micr...
Each C2Card provides an overview of the knowledge of multiple pathway databases from the perspective of a specific gene, EC number or reaction of interest. A C2Card answers the basic question of which databases contain the entity of interest. Importantly, each card provides a concise overview of...
The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale ...
History of network-based metabolic pathway analyses Network-based metabolic pathway analysis has a relatively short history. A mathematical formalism for analyzing biochemical pathways was developed in the late 1980s [9]; from a database that contained enzyme and metabolite information, the algorithm ge...
F. Metabolic pathway engineering for production of 1,2-propanediol and 1-propanol by Corynebacterium glutamicum. Biotechnol. Biofuels 8, 91 (2015). Article PubMed PubMed Central CAS Google Scholar Nakamura, C. E. & Whited, G. M. Metabolic engineering for the microbial production of 1,3-...
It is a reference database for metabolic pathway analysis also. So, we performed KEGG pathway analysis for weighted differentially coexpressed gene (WDCG) obtained from gene expression pairs (Acute–Chronic, Chronic–Nonprogressor, and Nonprogressor–Acute) to obtain whether any gene is significant...
KEGG pathway database - Kyoto University Bioinformatics Centre. [http://www.genome.jp/kegg/pathway.html], BioModels Database. [http://www.ebi.ac.uk/biomodels], MetaCyc Encyclopedia of Metabolic Pathways. [http://metacyc.org], Sridhar P, Kahveci T, Ranka S:An iterative algorithm for metab...
After the first reaction is inserted into the pathway, the ant repeat five operations (lines 10 to 17). Initially, the ant identifies all the reactionsrfor which the substrates are inCk, filtering those that are already in the pathwayπk. Then, it chooses one reactionr∈raccording to its...
The KEGG Pathway database is a valuable collection of metabolic pathway maps. Nevertheless, the production of simulation capable metabolic networks from KEGG Pathway data is a challenging complicated work, regardless the already developed tools for this scope. Originally used for illustration purposes, ...
Database (Metacyc) pathway abundance predictions51. Results were visualized in statistical analysis of taxonomic and functional profiles (STAMP) version 2.1.352and tested using Welch’sttest for two groups, MHO vs. MUO. All predictions were corrected for multiple testing (Benjamini–Hochberg method,...