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 literaturehttp://thebiogrid.org/

BRENDA [54]A database of molecular and biochemical information on enzymeshttp://www.brenda-enzymes.org/

ChEBI [55]A database and ontology of molecular entitieshttp://www.ebi.ac.uk/chebi/

ChemSpider [56]A database of chemicals. It contains more than 34 million unique molecules from over 450 data sourceshttp://www.chemspider.com/

DIP [57]A manually curated database of experimentally elucidated interactions between proteinshttp://dip.doe-mbi.ucla.edu/dip/

EcoCyc [58]A database of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways in Escherichia coli K-12, curated from the literaturehttp://ecocyc.org/

GenBank [59]A comprehensive database of publicly available nucleotide sequenceshttp://www.ncbi.nlm.nih.gov/genbank/

Gene Ontology [60]A database of annotations of genes and gene products for aiming to provide a common language to make data machine readablehttp://geneontology.org/

IntAct [61]A database of molecular interaction derived from literature curation or direct user submissionshttp://www.ebi.ac.uk/intact/

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 PANTHERhttp://www.ebi.ac.uk/interpro/

KEGG [63]An integrated database resource consisting of seventeen databases which are categorized into systems, genomic, chemical, and health informationhttp://www.genome.jp/kegg/

KNApSAcK [64, 65]An integrated database constituting a database of manually curated metabolite-plant species, metabolic pathways, biological activities, and so forth for metabolomics studieshttp://kanaya.naist.jp/KNApSAcK_Family/

MetaboLights [66]A data repository for metabolomics experiments and obtained informationhttp://www.ebi.ac.uk/metabolights/

MetaCyc [67]A metabolic database containing metabolic pathways, enzymes, metabolites, and reactions from many organismshttp://metacyc.org/

OMIM [68]A database of diseases with human genes and genetic conditionshttp://www.ncbi.nlm.nih.gov/sites/entrez?db=omim

ProteomeScout [69]A database of proteins and post-translational modificationshttps://proteomescout.wustl.edu/

PubChem [70]A database of chemical molecules and their activitieshttp://pubchem.ncbi.nlm.nih.gov/

Reactome [71, 72]A database of human biological processes authored by expert biologistshttp://www.reactome.org/

RegulonDB [73]A database of regulatory network and operon organization in Escherichia coli K-12http://regulondb.ccg.unam.mx/

STRING [74]A database of protein interactions (direct or indirect) derived from manual curation or text mininghttp://string-db.org/

TAIR [75]A comprehensive database of information and materials of Arabidopsis thalianahttps://www.arabidopsis.org/

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 versionhttp://genexplain.com/transfac-db

TRANSPATH [77]A database of mammalian signal transduction and metabolic pathwayshttp://genexplain.com/transpath-db

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)http://www.uniprot.org/