BioMed Research International / 2015 / Article / Tab 1

Review Article

A Glimpse to Background and Characteristics of Major Molecular Biological Networks

Table 1

A list of selected databases related to omics networks.

Database nameShort descriptionWeb address

BioGRID [53]A database of proteins, genes, and posttranslational modifications curated from the scientific literature

BRENDA [54]A database of molecular and biochemical information on enzymes

ChEBI [55]A database and ontology of molecular entities

ChemSpider [56]A database of chemicals. It contains more than 34 million unique molecules from over 450 data sources

DIP [57]A manually curated database of experimentally elucidated interactions between proteins

EcoCyc [58]A database of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways in Escherichia coli K-12, curated from the literature

GenBank [59]A comprehensive database of publicly available nucleotide sequences

Gene Ontology [60]A database of annotations of genes and gene products for aiming to provide a common language to make data machine readable

IntAct [61]A database of molecular interaction derived from literature curation or direct user submissions

InterPro [62]A database for classification and analysis of protein sequences. It includes resources from PROSITE, HAMAP, Pfam, PRINTS, PRoDom, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, CATH-Gene3D, and PANTHER

KEGG [63]An integrated database resource consisting of seventeen databases which are categorized into systems, genomic, chemical, and health information

KNApSAcK [64, 65]An integrated database constituting a database of manually curated metabolite-plant species, metabolic pathways, biological activities, and so forth for metabolomics studies

MetaboLights [66]A data repository for metabolomics experiments and obtained information

MetaCyc [67]A metabolic database containing metabolic pathways, enzymes, metabolites, and reactions from many organisms

OMIM [68]A database of diseases with human genes and genetic conditions

ProteomeScout [69]A database of proteins and post-translational modifications

PubChem [70]A database of chemical molecules and their activities

Reactome [71, 72]A database of human biological processes authored by expert biologists

RegulonDB [73]A database of regulatory network and operon organization in Escherichia coli K-12

STRING [74]A database of protein interactions (direct or indirect) derived from manual curation or text mining

TAIR [75]A comprehensive database of information and materials of Arabidopsis thaliana

TRANSFAC [76]A manually curated database of eukaryotic transcription factors, their experimentally elucidated binding sites and DNA binding profiles. It needs a license for the up-to-date version

TRANSPATH [77]A database of mammalian signal transduction and metabolic pathways

UniProtKB [78]A database of functional information on proteins. It consists of UniProtKB/Swiss-Prot (manually annotated, reviewed) and UniProtKB/TrEMBL (automatically annotated, not reviewed)