GeneBrowser 2: an application to explore and identify common biological traits in a set of genes

BMC Bioinformatics

Table 1 List of integrated databases and methods applied to extract data

Type	Name	GeNS	Real-time data retrieval	URL
Gene	Ensembl	X		http://www.ensembl.org/
	HGNC	X		http://www.genenames.org/
	UniGene		X	http://www.ncbi.nlm.nih.gov/unigene/
	Entrez Gene	X	X	http://www.ncbi.nlm.nih.gov/gene/
	RefSeq	X		http://www.ncbi.nlm.nih.gov/refseq/
	KEGG Genes	X	X	http://www.kegg.jp/
Protein	UniProtKB	X	X	http://www.uniprot.org/
	Gene3D	X		http://gene3d.biochem.ucl.ac.uk/Gene3D/
	PDB	X	X	http://www.pdb.org/
	IntAct	X	X	http://www.ebi.ac.uk/intact/
Homology	InterPro	X	X	http://www.ebi.ac.uk/interpro/
	PFam	X		http://pfam.sanger.ac.uk/
	PRINTS	X		http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS
	PROSITE	X	X	http://www.expasy.ch/prosite/
	PANTHER	X		http://www.pantherdb.org/
	ProDom	X		http://prodom.prabi.fr/
Pathway	Reactome	X		http://www.reactome.org/
	KEGG Pathway	X	X	http://www.kegg.jp/
	BioCyc	X	X	http://www.biocyc.org/
Drug	KEGG Drug	X	X	http://www.kegg.jp/
	PharmGKB	X	X	http://www.pharmgkb.org/
	DrugBank	X		http://www.drugbank.ca/
Disease	OMIM	X		http://www.ncbi.nlm.nih.gov/omim/
	Orphanet	X		http://www.orpha.net/
Enzyme	EC	X		http://www.biochem.ucl.ac.uk/bsm/dbbrowser/protocol/ecenzfrm.html
	Brenda	X		http://www.brenda-enzymes.org/
Bibliography	PubMed	X	X	http://www.ncbi.nlm.nih.gov/pubmed/
Ontology	Gene Ontology	X		http://www.geneontology.org/

ISSN: 1471-2105