Applying the dGene list to CNVs in 46 breast cancer tumours.

<p><b>A,</b> 5421 CNVs were detected in 1752 druggable genes across the sample. The 20^th (0.7×) and 80^th (1.5×) percentiles served as cutoffs. <b>B,</b> Gains only (>1.5×). <b>C,</b> Losses only (<0.7×). <b>D,</b> Displaying PTEN family CNV values. <i>TPTE2</i> is the most frequently altered. Cutoffs are relaxed to <0.85× and >1.15× for display purposes.</p

Summary of the dGene list.

<p>The following references outline primary database construction: GPCRDB (Ref. 8; url: <a href="http://www.gpcr.org/7tm/" target="_blank">http://www.gpcr.org/7tm/</a>); MEROPS (Ref. 7; url: <a href="http://merops.sanger.ac.uk/" target="_blank">http://merops.sanger.ac.uk/</a>); KinBase (Ref. 11; url: kinase.com); NucleaRDB (Ref. 6; url: <a href="http://www.receptors.org/nucleardb/" target="_blank">http://www.receptors.org/nucleardb/</a>); Uniprot (Ref. 9; url: <a href="http://www.uniprot.org" target="_blank">www.uniprot.org</a>); Gene Ontology (Ref. 10; url: <a href="http://www.geneontology.org" target="_blank">www.geneontology.org</a>). All URLs valid as of 2/26/2013.</p

Rationale and process for construction of the dGene list.

<p><b>A</b>, Druggability serves as a rational screen in a hypothetical pipeline for reducing a raw gene list to an experimentally workable number. <b>B</b>, Lung cancer drugs in the pipeline classified by target type, with some target types considered broadly druggable and included in dGene. <b>C</b>, NHRs required a simple workflow. Russ <i>et al,</i> 2005 and NucleaRDB <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067980#pone.0067980-Vroling1" target="_blank">[6]</a> provided input. One gene mapped to neither the NCBI gene nor synonyms list. Six genes were identified in only one source and were manually checked against UniProt and Gene Ontology (GO) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067980#pone.0067980-Apweiler1" target="_blank">[9]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067980#pone.0067980-Blake1" target="_blank">[10]</a>. None could be confirmed as NHRs, leaving the final class with 48 members. <b>D</b>, The elaborated workflow for proteases is analogous to that of the NHRs and other classes. Because UniProt served as input, curation involved searching the primary literature in addition to querying GO.</p