The Molecular Ancestry Network (MANET) database is a
bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...
database
In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and a ...
that maps evolutionary relationships of protein architectures directly onto biological networks. It was originally developed by Hee Shin Kim, Jay E. Mittenthal and
Gustavo Caetano-Anolles in the Department of Crop Sciences of the
University of Illinois at Urbana-Champaign
The University of Illinois Urbana-Champaign (UIUC, U of I, Illinois, or University of Illinois) is a public land-grant research university in the Champaign–Urbana metropolitan area, Illinois, United States. Established in 1867, it is the f ...
.
MANET traces for example the ancestry of individual metabolic enzymes in
metabolism
Metabolism (, from ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the co ...
with bioinformatic, phylogenetic, and statistical methods. MANET currently links information in the Structural Classification of Proteins (
SCOP
A ( or ) was a poet as represented in Old English poetry. The scop is the Old English counterpart of the Old Norse ', with the important difference that "skald" was applied to historical persons, and scop is used, for the most part, to designat ...
) database, the metabolic pathways database of the Kyoto Encyclopedia of Genes and Genomes (
KEGG
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis ...
), and phylogenetic reconstructions describing the evolution of protein fold architecture at a universal level. The database has been updated to reflect evolution of metabolism at the level of protein fold families. MANET literally "paints" the ancestries of enzymes derived from rooted phylogenetic trees directly onto over one hundred metabolic pathways representations, paying homage to one of the fathers of
impressionism
Impressionism was a 19th-century art movement characterized by visible brush strokes, open Composition (visual arts), composition, emphasis on accurate depiction of light in its changing qualities (often accentuating the effects of the passage ...
. It also provides numerous functionalities that enable searching specific protein folds with defined ancestry values, displaying the distribution of enzymes that are painted, and exploring quantitative details describing individual protein folds. This permits the study of global and local metabolic network architectures, and the extraction of evolutionary patterns at global and local levels.
A statistical analysis of the data in MANET showed for example a patchy distribution of ancestry values assigned to protein folds in each subnetwork, indicating that evolution of metabolism occurred globally by widespread recruitment of enzymes.
[ MANET was used recently to sort out enzymatic recruitment processes in metabolic networks and propose that modern metabolism originated in the ]purine
Purine is a heterocyclic aromatic organic compound that consists of two rings (pyrimidine and imidazole) fused together. It is water-soluble. Purine also gives its name to the wider class of molecules, purines, which include substituted puri ...
nucleotide metabolic subnetwork.evolution
Evolution is the change in the heritable Phenotypic trait, characteristics of biological populations over successive generations. It occurs when evolutionary processes such as natural selection and genetic drift act on genetic variation, re ...
.
External links
Molecular Ancestry Network (MANET) database
References
{{reflist, 2
Biochemistry databases
Metabolomic databases