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
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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
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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
In 1990, the first great stride of genetics took place. This was called the Human Genome Project, a large-scale operation that was designed to understand the human genome (genetic structure). Since its commencement, there have been many leaps and bounds that have taken place. For certain genetic issues that we once knew nothing about, we no...
The two different alleles present in the could be due to the effect of evolution and natural selection because the same can be found in chimps.4 The PV92 locus does not code for any protein but rather involves an Alu element that is 300-bp long. A person with the “+” allele would have the Alu element, making that sequence longer while those with the “-“ allele don’t have the element and would have a shorter sequence. This locus can be found on chromosome 16.3 There are multiple Alu sequences found among primate genomes but there are human specific sequences such as the one found on the PV92 locus.1 In the experiment, student DNA was collected from cheek cells and PCR was used to target the loci and amplify the region of DNA. In the taster gene, after amplification, a restriction digest was performed to differentiate between the two alleles. The digest was able to show differentiation because those with the “T” allele would have two bands from gel electrophoresis and those with “t” would have one band because the restriction enzyme doesn’t cut it.
When horrific crimes occur in large cities, many of them can be chalked up to gang violence or to the larger population of that specific city. But when horrific crimes happen in small cities like Lincoln, Nebraska, people begin to ask questions like who did this and why. In 1958, a nineteen year old man named Charles Starkweather put the entire state of Nebraska and possibly the entire nation in a state of terror. With his murder spree taking only three days, Starkweather had collected a body count of ten bodies, including two teenagers and a young child. Understanding Starkweather’s past and state of mind begins to answer the second question of why.
-Reilly Philip. Is It In Your Genes. Cold Spring Harbor Laboratory Press. 2004: 223-228. Print
In 1993 a consortium of researchers who worked on the DNA samples from families in the Lake Maracaibo region of Venezuela, an area with a high density of HD and significant consanguinity, reported the successful discovery of the gene responsible for the occurrence of this disease, present in chromosome 4 and named it as IT15 (Interesting transcript #15). IT15 later called as the Huntingtin gene (HTT) [2]. HTT is ~10 kilobases (kb) long and translated into a protein of 3144 amino acids with anticipated molecular mass of 348 kDa. Huntigtin protein is expressed in in human and all mammalian cells, where brain and testis has the highest concentration; liver...
Schulman, Joshua M., and David E. Fisher. "Abstract." National Center for Biotechnology Information. U.S. National Library of Medicine, 28 Aug. 0005. Web. 24 Apr. 2014.
Lewis, Ricki, (2014), Human Genetics, 11th Edition, Chapter 12. Gene Mutation. [VitalSource Bookshelf Online]. Retrieved from
Segal, E. A., Cimino, A. N., Gerdes, K. E., Harmon, J. K., & Wagaman, M. (2013). A
The evolution of studying and documenting genetic diseases in the scientific community has been one of exponential growth, this is important because it helps communities
The simulation study showed that the additional information of CNP could increase the accuracy of predicted genotypic value, compared to using SNP information alone in an association study. The accuracy was heavily dependent on the heritability of CNP phenotypes (correlation of CNP genotype and phenotype) (Table 3). The higher accuracy of the prediction with CNP information might also result in smaller mean squared errors of prediction (Table 4)’.
This case study is intended to analyze the movie When a Man Loves a Woman, and to provide worst and best case scenarios for treatment. This film depicts a family that is struggling with a family member’s alcoholic dependency. The mother, Alice Green, is a school counselor who has an addiction to alcohol that is causing her to experience problems in her life as a result of her use. Her husband, Michael Green, is an airline pilot that is very protective Alice and often steps in and takes over for Alice, even in her role as a mother. Alice has two children, Jess and Casey, which also bear witness to their mother’s deterioration from alcohol addiction.
Campbell N. A., Reece L. A., Cain M. L., Wasserman S. A., Minorsky P. V. and Jackson R. B. (2008). Regulation of Gene Expression
Genetically influenced traits tend to be polygenic in character, involving many genes acting in concert to produce a certain response. Therefore, association of one gene with one behavior is usually only partially conclusive. Behavior depends on the interaction of multiple gene sequences with environmental influences. ...
more than half the variation was found to be due to heredity. Among these traits were
...ary part in genotypes of potential interest that human geneticists breeders, as well as evolutionary geneticists are investigating. However, although we have the capability to unravel experiments that the founders of quantitative genetics would have never imagined, but their basic, un-computational machinery that they developed is most easily adaptable to the latest analyses that will be needed. We are far from ‘letting-go’ molecular biologists from the mathematical techniques/systems, because this age in respect to genomics has been forced into accepting gratitude due to the major importance of quantitative methods as opposed to the new molecular genetics. As geneticists tend to map molecular variation as well as genomic data, quantitative genetics will be moving to the front position because of its relevance in this age of rapid advancement in molecular genetics.