Table 1.

SynDB protein annotations and cross-referenced molecular databases

Protein annotations	Cross-referenced databases
Gene name	NCBI Entrez Gene (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene)
Species	NCBI Taxonomy DB (ftp://ftp.ncbi.nih.gov/pub/taxonomy/)
Sequences	GenBank (http://www.ncbi.nlm.nih.gov/)
Chromosomal location	GoldenPath (http://hgdownload.cse.ucsc.edu/goldenPath/)
GO functional category	Gene Ontology (GO) (http://www.ebi.ac.uk/GOA/)
Protein domain	InterPro (http://www.ebi.ac.uk/interpro/)
Structure	Protein Data Bank (PDB) (http://www.rcsb.org/pdb/) ModBase (http://salilab.org/modbase-cgi)
Gene expression	GEO (http://www.ncbi.nlm.nih.gov/geo/) BodyMap-Xs (http://bodymap.jp)
Antisense transcripts	NATsDB (http://natsdb.cbi.pku.edu.cn/)
Post-transcriptional modification	dbPTM (http://dbptm.mbc.nctu.edu.tw/)
Protein family	Ensembl Family (http://www.ensembl.org/Homo_sapiens/familyview)
Pathway	KEGG (http://www.genome.jp/kegg/)
Protein–protein interaction	PPID (http://www.anc.ed.ac.uk/mscs/PPID/) DIP (http://dip.doe-mbi.ucla.edu/dip/Download.cgi)
Disease association	OMIM (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM)
References	PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi)