User: Denise - Open Targets

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4,030
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Location:
UK, Hinxton, EMBL-EBI
Website:
http://www.ebi.ac.uk/a...
Twitter:
@deniseOme
Scholar ID:
Google Scholar Page
Last seen:
34 minutes ago
Joined:
2 years, 11 months ago
Email:
r*******@yahoo.com

I design and deliver the Outreach activities for Open Targets at EMBL-EBI with my love of genomes, user support, training, and communication in genomics and bioinformatics. Exploring aspects of early drug discovery and disease biology. Previously worked in Ensembl and Ensembl Genomes, GENCODE, EUCOMM and Pig Genome projects, with post-doctorate in human population genetics (at the Wellcome Trust Sanger Institute) and sex chromosome evolution (at the Australian National University).

Posts by Denise - Open Targets

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Comment: C: Do multiple SNPs exist in same chromosome to be called allele?
... I've got a population genetics bias, so when I read a SNP has two alleles, I think of the alleles in the population as a whole, rather than the two alleles in a (diploid) genome. However if an individual has a trisomy, they will have three alleles. ...
written 4 hours ago by Denise - Open Targets4.0k
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Comment: C: Do multiple SNPs exist in same chromosome to be called allele?
... An allele is a state, form a type that varies at one locus within a given sample/population. They are not one single base only. Insertions (or deletion) of several bases at one locus (in one individual within a population) mean that at that locus the alleles with be the string of bases (the inser ...
written 5 hours ago by Denise - Open Targets4.0k
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Comment: C: Do multiple SNPs exist in same chromosome to be called allele?
... Although the sheer majority of single nucleotide polymorphism contains two alleles only, there can be loci with 3 alleles as well e.g. [rs2032582][1] and [rs3091244][2]. [1]: http://www.ensembl.org/Homo_sapiens/Variation/Explore?r=7:87530802-87531802;v=rs2032582;vdb=variation;vf=1453429 [2]: h ...
written 5 hours ago by Denise - Open Targets4.0k
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Answer: A: pathway analysis tools
... These are some I've come across with: [OminPath][1] with a Python module, [Reactome][2] and [GSEA][3]. [1]: http://omnipathdb.org/ [2]: http://reactome.org/ [3]: http://software.broadinstitute.org/gsea/index.jsp ...
written 5 hours ago by Denise - Open Targets4.0k
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Comment: C: How do you use Biomart to get info about genes that didn't originate from Ensemb
... No, don't go looking for an alternative to BioMart! It's such a great, easy to use tool. In addition to @Jean-Karim Heriche's answer, note that XMs are RefSeq mRNA predicted IDs. So that's the external reference ID you need to select. Also, leave the versioning out: so use XM_415059 but *not* XM_41 ...
written 7 hours ago by Denise - Open Targets4.0k
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Comment: C: Why genomic information shown in UCSC/Ensembl browser for a specific gene is dif
... Can you give us some examples of genes whose coordinates from the bed file don't match what you see on the UCSC and Ensembl browsers? Things to double check: same assembly, same version of the GENCODE gene set, whether you are dealing with the 'canonical' (whatever that means) or longest transcript, ...
written 1 day ago by Denise - Open Targets4.0k
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Comment: C: awesome cancer genomics
... Can you define awesome? Would [COSMIC][1] help? [1]: http://cancer.sanger.ac.uk/cosmic ...
written 6 days ago by Denise - Open Targets4.0k
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Answer: A: What is the difference between hg19 v9 vs hg19
... v9 corresponds to GENCODE [Version 9][1] of HG19 (=GRCh37), May 2011 data freeze. GENCODE is the set of annotated genes and transcripts for ENCODE and other projects. The annotation is/was ongoing, hence the different versions. For HG19, the last GENCODE version was 19, July 2013 data freeze. [1 ...
written 7 days ago by Denise - Open Targets4.0k
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Answer: A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
... I have not worked with BRCA diagnostics but [Open Targets][1] combines somatic and germline data from several resources (most if not all are manually curated variants for our [genetic associations][2]). We also have a variety of information in the profile page of the gene of interest e.g. [BRCA1][3] ...
written 8 days ago by Denise - Open Targets4.0k
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Comment: C: Fantom5 enhancers to TSS_distance
... Have you seen this [file][1]? There is also sets of enhancer and TSS-enhancer association data available for [download][2]. The latter was based on the [An atlas of active enhancers across human cell types and tissues][3] paper. Ensembl has also got the TSS and enhancers from Fantom5 as [other Regul ...
written 13 days ago by Denise - Open Targets4.0k

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Teacher 29 days ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
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Popular Question 3 months ago, created a question with more than 1,000 views. For Open Targets, validating targets for drug development in the treatment of diseases.
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