User Case Study

1463 Words3 Pages

Isar Nassiri
User Case #1
A USC researcher is interested in the roles of coregulators in steroid hormone regulation of transcription in cancer cells and would like to write a grant proposal on this topic. The two key coregulators of interests are Hic-5 and G9a. As he is preparing the proposal, he hopes to find information about the following questions:
Answer
1. The known post-translational modifications of the two genes
You can answer to this question by searching the specific databases. You can use the PhosphoSitePlus® (PSP) resource to find post-translational modifications of the two genes (http://www.phosphosite.org/homeAction.action). PhosphoSitePlus provides comprehensive information and tools for the study of protein post-translational …show more content…

SNPs in the two genes that might impact their functions. 

An SNPs might impact on the functions of gene if the abundance of a gene transcript is directly modified by existence of the polymorphism. In this case transcript abundance of indicate gene might be considered as a quantitative trait that its association with SNP can be studied by eQTL analysis (acronym of expression quantitative trait loci).
GTEX portal (http://www.gtexportal.org/home/) helps you to retrieve the available information about the impact of SNPs on the function of indicated gene (transcript abundance). The privilege of GTEX portal in comparison to the other resources is its ability to search and functional analysis of SNPs, simultaneously.
To this end, you can enter the name of a gene (e.g. TGFB1I1) in the field of Genetic Association to retrieve all related functional SNPs. You can use the Multi-tissue eQTL comparison to consider the functional impact of indicated SNP in all tissues. In figure 3 you can see the example result for the functional impact of rs4889661 in TGFB1I1. Figure 3. The output of multi-tissue eQTL comparison of the functional impact of rs4889661 in different tissues. The m-value presents the posterior probability of the existence of an eQTL effect in indicated tissue. The m-value ranges between 0 and 1, and large m-value (e.g. > 0.8) is predictor of positive eQTL …show more content…

The expression data for CEU and CHB families can be obtained from SANGER GENEVAR project (ftp://ftp.sanger.ac.uk/pub/genevar/) and in the Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/ accession number GSE17080). HapMap genotype data are publicly available at (http://www.hapmap.org).
For this analysis we prefer GGtools Bioconductor package. Genevar and SNPexp could be an alternative web tools for calculating and visualizing correlation between HapMap genotypes and gene expression levels but are no longer available (Holm, et al., 2010; Yang, et al., 2010).
First, we should find the location of indicated SNPs on the human genome by using the genome variation server (GVS) (Kim, et al., 2009). We use rs ID to search the rs1458836 and rs7933235, and set up “merge samples and variations” parameter to “C – combined samples with combined variations”. As you can see in the figure 4, they locate on the long arm of chromosome 11.

Figure 4. The location of indicated rs1458836 and rs7933235 on the human genome by using the genome variation server

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