dtlink_db_clue_sti: Drug-Target Annotation Resources

In yduan004/signatureSearchData: Datasets for signatureSearch package

Drug-Target Annotation Resources

Description

This is a SQLite database containing drug-target links (drug names to gene SYMBOL ids) obtained from DrugBank, CLUE, and STITCH annotation databases.

Details

It is an intermediate database used for functionality in the signatureSearch software package to get target genes/proteins of query drugs in DrugBank (https://www.drugbank.ca/), CLUE (https://clue.io/) and STITCH (http://stitch.embl.de/) databases.

The target proteins of drugs are mapped to their encoding genes by using identifier mapping resources from R/Bioconductor such as the org.Hs.eg.db annotation package. Thus, the drug-target links in this database are drug names to gene SYMBOLs mapping.

The STITCH database provides confidence scores for each drug-target interaction. Only interactions with confidence scores >=0.7 were selected.

The drug-target interaction annotations from the above three databases are combined. To minimize noise, e.g. from promiscuous binders, drugs with more than 100 distinct targets are removed. Similarly, targets with more than 100 annotated drugs are excluded.

See Also

get_targets

Examples

library(ExperimentHub)
eh <- ExperimentHub()
qr <- query(eh, c("signatureSearchData", "dtlink_db_clue_sti"))
dtlink <- eh["EH3228"]
# dtlink <- eh[["EH3228"]]

yduan004/signatureSearchData documentation built on April 7, 2023, 4:12 a.m.