| Literature DB >> 26876983 |
Adam D DePriest1, Michael V Fiandalo2, Simon Schlanger3, Frederike Heemers3, James L Mohler2, Song Liu4, Hannelore V Heemers5.
Abstract
Androgen receptor (AR) is a ligand-activated transcription factor that is the main target for treatment of non-organ-confined prostate cancer (CaP). Failure of life-prolonging AR-targeting androgen deprivation therapy is due to flexibility in steroidogenic pathways that control intracrine androgen levels and variability in the AR transcriptional output. Androgen biosynthesis enzymes, androgen transporters and AR-associated coregulators are attractive novel CaP treatment targets. These proteins, however, are characterized by multiple transcript variants and isoforms, are subject to genomic alterations, and are differentially expressed among CaPs. Determining their therapeutic potential requires evaluation of extensive, diverse datasets that are dispersed over multiple databases, websites and literature reports. Mining and integrating these datasets are cumbersome, time-consuming tasks and provide only snapshots of relevant information. To overcome this impediment to effective, efficient study of AR and potential drug targets, we developed the Regulators of Androgen Action Resource (RAAR), a non-redundant, curated and user-friendly searchable web interface. RAAR centralizes information on gene function, clinical relevance, and resources for 55 genes that encode proteins involved in biosynthesis, metabolism and transport of androgens and for 274 AR-associated coregulator genes. Data in RAAR are organized in two levels: (i) Information pertaining to production of androgens is contained in a 'pre-receptor level' database, and coregulator gene information is provided in a 'post-receptor level' database, and (ii) an 'other resources' database contains links to additional databases that are complementary to and useful to pursue further the information provided in RAAR. For each of its 329 entries, RAAR provides access to more than 20 well-curated publicly available databases, and thus, access to thousands of data points. Hyperlinks provide direct access to gene-specific entries in the respective database(s). RAAR is a novel, freely available resource that provides fast, reliable and easy access to integrated information that is needed to develop alternative CaP therapies. Database URL: http://www.lerner.ccf.org/cancerbio/heemers/RAAR/search/.Entities:
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Year: 2016 PMID: 26876983 PMCID: PMC4752970 DOI: 10.1093/database/bav125
Source DB: PubMed Journal: Database (Oxford) ISSN: 1758-0463 Impact factor: 3.451
Figure 1.Flexibility in intraCaP DHT biosynthesis pathways. Schematic of principal androgen biosynthesis pathways and core enzymes that lead to DHT production in CaP cells. Italicized text, deregulated gene expression under ADT; boldface text, genomic alterations under ADT. Note that proteins involved in androgen transport and androgen degradation are not considered.
Overview of RAAR content
| RAAR section | Entries (number) | Hyperlinked databases (number) | # Data points |
|---|---|---|---|
| Pre-receptor level | 55 | 24 | >1000/entry |
| Post-receptor level | 274 | 25 | >1000/entry |
| Other resources | 36 | 36 | >1000/entry |
Overview of databases to which RAAR provides entry-specific access and the types of information they provide
| Database | URL | Gene function | Clinical relevance | Resources | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Basic gene info | Gene structure | Gene functionality | Regulation of GEX | Interactome | Disease | Therapeutics | Reagents | References | ||
| Ensembl | x | x | x | x | ||||||
| HGNC | x | |||||||||
| APPRIS | x | x | x | |||||||
| COSMIC | x | x | ||||||||
| ENCODE | x | x | x | x | x | |||||
| NCBI Gene | x | x | x | |||||||
| NCBI Nucleotide | x | x | x | |||||||
| NCBI Protein | x | x | x | |||||||
| UniProt | x | x | x | x | ||||||
| ProteinDataBank | x | x | x | x | ||||||
| Reactome | x | x | ||||||||
| neXtprot | x | x | x | x | ||||||
| Domain mapping mutations | x | x | ||||||||
| Atlas (Cyto)genetics | x | x | x | x | ||||||
| GenAtlas | x | x | x | x | x | |||||
| Oncomine | x | x | ||||||||
| cBioPortal | x | x | x | x | ||||||
| Medicalgenomics | x | x | x | |||||||
| NCBI dbSNP | x | x | x | |||||||
| SNPper | x | x | ||||||||
| PharmGKB | x | x | x | |||||||
| GeneProf | x | x | x | x | x | |||||
| NURSA | x | x | x | x | ||||||
| GeneCards | x | x | x | x | x | x | x | x | ||
| Labome | x | |||||||||
Figure 2.Sample of the information that RAAR provides for each of its entries. For each entry, RAAR allows cycling between information on different aspects of gene function, clinical relevance and availability of resources. Examples of representative questions (Qs) that RAAR answers are also shown.
Figure 3.Screenshot of autocomplete function that lists eligible search terms (A) and basic RAAR search form and sample query result (B) for pre-receptor database.
Figure 4.Screenshot of autocomplete function that lists eligible search terms (A) and basic RAAR search form and sample query result (B) for other resources database.