--- title: To be, or not to be, a drug target gene description: Is your gene a potential therapeutic drug target? There are several steps that could start your investigation, and watch out for eaglecurate in May 2017. image: https://www.eaglegenomics.com/hubfs/Imported_Blog_Media/human_inset_03.png --- - [Home](https://www.eaglegenomics.com) - What We Do - [e\[datascientist\]](https://www.eaglegenomics.com/what-we-do/e-datascientist-platform) - [e\[exploration\]](https://www.eaglegenomics.com/what-we-do/e-datascientist-platform/e-exploration) - [e\[biology\]](https://www.eaglegenomics.com/what-we-do/e-datascientist-platform/e-biology) - [e\[datascience\]](https://www.eaglegenomics.com/what-we-do/e-datascientist-platform/e-data-science) - [e\[sdk\]](https://www.eaglegenomics.com/what-we-do/e-datascientist-platform/e-software-development-kit) - [e\[marketplace\]](https://www.eaglegenomics.com/what-we-do/e-datascientist-platform/e-marketplace) - [Microbial Strain Characterization](https://www.eaglegenomics.com/microbial-strain-characterisation) - [Networking Microbiome Science](https://www.eaglegenomics.com/what-we-do/networking-microbiome-science) - [About Us](https://www.eaglegenomics.com/about-us) - [Customers](https://www.eaglegenomics.com/customers) - [News](https://www.eaglegenomics.com/news) - [Contact Us](https://www.eaglegenomics.com/contact-us) [Skip to content](https://www.eaglegenomics.com/news/to-be-or-not-to-be-a-drug-target-gene#main-content) [![EG-01](https://www.eaglegenomics.com/hubfs/EG-01.svg "EG-01")](https://www.eaglegenomics.com/) [Get in touch](https://www.eaglegenomics.com/contact-us) - [Home](https://www.eaglegenomics.com/?hsLang=en) - [News](https://www.eaglegenomics.com/news) - Blog Mar 15, 2017 4:31:00 PM # To be, or not to be, a drug target gene   ## To be, or not to be, a drug target gene I have a drug target gene (or gene list) and I want to do a preliminary investigation to learn more about my gene and gene products of interest. But where do I start? Which genomic, biological or bioinformatics resources should I use? There are so many databases available. Here are just a few to get you started, and a clue to the data you can find. ## Start with the gene For an initial look at your gene and its products, why not visit [Ensembl](http://www.ensembl.org/index.html). Enter a query for your gene, remember that you may be querying with the synonym of approved gene symbol (for example FANCS is a synonym of BRCA1), so the results may not be exactly what you were expecting to see! Once you have identified your gene, take a note of the approved symbol as this will help your further database queries. Also note that Ensembl have assigned identifiers for the gene (ENSG), transcript (ENST) and protein (ENSP), these identifiers will be used to map data within Ensembl and between Ensembl and other databases.  ![Screen Shot 2017-03-13 at 14.37.59.png](https://www.eaglegenomics.com/hs-fs/hubfs/Imported_Blog_Media/Screen%20Shot%202017-03-13%20at%2014_37_59.png?width=848&height=131&name=Screen%20Shot%202017-03-13%20at%2014_37_59.png) Ensembl [Gene](http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000012048;r=17:43044295-43170245) details On the gene page, Ensembl will provide genomic data, including the overall gene structure (how many exons, size of the CDS, etc) number of transcripts and proteins. There are also links to the phenotypes associated to the gene and the SNPs within the gene, as well as a full table of variants. Orthologues, paralogs and protein family members are also provided to give an overview of the taxonomy and ancestral “development” of your gene. Some of our customers have taken advantage of our expert knowledge of Ensembl and have a customised installation that allows them to visualise and search their genome data. If you are interested in **eagle**nsembl then please contact info@eaglegenomics.com. ## Transcripts and proteins From the gene page there is a table of transcripts and their biotype (protein coding, processed transcript etc). For transcripts there is haplotype data; some SNPs tend to occur together and inform the protein generating multiple protein forms, these are haplotypes. The consequence of the amino acid change, the overall frequency of that haplotype in the 1000 Genomes group is also provided. Interestingly, the reference genome may not encode the most frequent protein form.  ![haplotypes.png](https://www.eaglegenomics.com/hs-fs/hubfs/Imported_Blog_Media/haplotypes.png?width=848&height=91&name=haplotypes.png) Ensembl [Haplotypes](http://www.ensembl.org/Homo_sapiens/Transcript/Haplotypes?db=core;g=ENSG00000012048;r=17:43044295-43170245;t=ENST00000357654) More detailed information about the protein can be found in [UniProt](http://www.uniprot.org/). This can be used to supplement with protein architecture and and amino sequence level annotations, as well as provide links to many other resources that may be of interest to you.  ![UniPot_protein_features.png](https://www.eaglegenomics.com/hs-fs/hubfs/Imported_Blog_Media/UniPot_protein_features.png?width=848&height=437&name=UniPot_protein_features.png)Protein features in [UniProt](http://www.uniprot.org/uniprot/P38398#showFeaturesViewer) ## Sequence variations We can augment the SNP information for each gene by also looking at the [GWAS catalogue](https://www.ebi.ac.uk/gwas/), [GWAS Central](http://www.gwascentral.org/), [DbSNP](https://www.ncbi.nlm.nih.gov/projects/SNP/), [openSNP](https://opensnp.org/) and [OpenTargets](https://www.opentargets.org/). From all these resources a full picture can be developed about sequence variation and association with phenotypes and disease. ![OPenTargets_variations.png](https://www.eaglegenomics.com/hs-fs/hubfs/Imported_Blog_Media/OPenTargets_variations.png?width=848&height=297&name=OPenTargets_variations.png)Gene vararions in [OpenTargets](https://www.targetvalidation.org/target/ENSG00000012048) ## Association with disease [OpenTargets](https://www.opentargets.org/) provides a search for a disease (and phenotype) and your target gene, the results include association score to summarise the strength of evidence for several attributes (somatic mutation, known drugs, pathways, RNA expression etc). ![opentargets_disease.png](https://www.eaglegenomics.com/hs-fs/hubfs/Imported_Blog_Media/opentargets_disease.png?width=848&height=566&name=opentargets_disease.png)Disease associations in [OpenTargets](https://www.targetvalidation.org/target/ENSG00000012048/associations) ## Tolerance to loss of function The [ExAC](http://exac.broadinstitute.org/) catalog can be used to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation. A probability of loss of function intolerance is provided, if intolerance is low (near 0) this suggests humans are able to cope where both copies of your gene of interest are non-functional. ## eQTLs By analyzing global RNA expression within individual tissues and treating the expression levels of genes as quantitative traits, variations in gene expression that are highly correlated with genetic variation can be identified as expression quantitative trait loci, or eQTLs. The Genotype-Tissue Expression ([GTEx](http://www.gtexportal.org/)) project provides a comprehensive identification of human eQTLs, providing a valuable basis on which to study the mechanism of that genes regulation. ![eQTL_GTEx.png](https://www.eaglegenomics.com/hs-fs/hubfs/Imported_Blog_Media/eQTL_GTEx.png?width=848&height=124&name=eQTL_GTEx.png)eQTLs from [GTEx](http://www.gtexportal.org/home/eqtls/byGene?geneId=BRCA1&tissueName=All). ## Clinical trials [ClinicalTrials.gov](https://clinicaltrials.gov/) is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world. You can search for your gene of interest to learn if has been involved in any registered clinical trials. ## Conclusion Following these suggestions, in addition to reading publications, will provide you with an excellent overview of your gene of interest, its structure, products, variants and their functions. Each gene can have thousands of sequence variations and you will be able to determine those that have a known association to your disease or phenotype of interest. Knowing if your target gene can tolerate loss of function is a good indication of safety and links to clinical trials will let you know if others are also interested in the same gene. Sounds like a good start to me! May 2017 will see the first iteration of a new product, [eaglecurate](https://www.eaglegenomics.com/eaglecurate/). The platform will provide functionality to link and automatically annotate data sources or specific R&D data with the appropriate semantic content which could reduce the time taken to manually investigate genes of interest. Watch this space! 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