Significance of Genomic Annotation
Genomic Annotation
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Significance of Multi-omics Studies
Multi-omics Multi-omics, variously called integrated omics, pan-omics, and trans-omics, aims to combine two or more omics data sets to aid in data analysis, visualization and interpretation to determine the mechanism of a biological process. Read More Complete the homework by adding your understanding as a comment below. Refer resources for more relevant information. NHGRI multi-omics workshop Review Article Answer in the comment section below
From my understanding genetic annotation is the process of identifying and describing the functions of genes and other elements in a genome. The goal of genetic annotation is to identify the elements within a functional genome and assign a function to the selected element.
ReplyDeleteGenetic annotation is the process of identifying the parts of the DNA that are functional. Through this scientists can identify the intron and extron parts of the DNA. This is important because if scientist want to specifically look for a part of a DNA that codes for a protein, through genome annotation they can find several and narrow down their list of DNA to search through. Genome annotation also identifies structural and functional annotation. This is very important because it allows scientists to find and specific part of the DNA and learn about its function, giving scientists a deeper insight into that specific part.
ReplyDeleteGenetic annotation is the process of identifying the parts of the DNA that are functional. Through this scientists can identify the intron and extron parts of the DNA. This is important because if scientist want to specifically look for a part of a DNA that codes for a protein, through genome annotation they can find several and narrow down their list of DNA to search through. Genome annotation also identifies structural and functional annotation. This is very important because it allows scientists to find and specific part of the DNA and learn about its function, giving scientists a deeper insight into that specific part. (Accidentally uploaded first response without connecting Google account)
ReplyDeleteGenetic annotation is finding the location and function of the genes. As databases improve, the annotation will become more accurate. GWAS is a study done to see how certain genetic variations affect people. Many of these studies are done to see how susceptible people are to disease or how effective certain drugs will be. It also sees which SNP or SNPs affect a particular part of the body.
ReplyDeleteI found it interesting in the video that during the regression analysis, the line's positioning determined the relationship of the results, leading to the P-Value. I also noted that the video mentioned Manhattan
ReplyDeleteplots which Dr. Ojha discussed previously. ~Cassina
I found it interesting that after collecting data from SNPs, scientists use a Manhattan plot to graphically represent -log10 p-values for each genetic variant tested in a GWAS. The x-axis of the plot represents the genomic position of the variant, and the y-axis represents the -log10 p-value. This Manhattan plot comes from the way the plot looks when many points are plotted on it, with the lines connecting the points resembling the skyline of Manhattan. I find it really unique how scientists came up with this graph concept to identify potential candidate genes for further investigation.
ReplyDeleteGenomic annotation is composed of 2-3 levels — these include structural annotation, functional annotation and comparison annotation. Once DNA has been computed using automatic processing of computers, the DNA file (SAM → BAM) can then be used to conduct structural and functional annotation. From what I know, the goal of structural annotation is to identify the regions/components of a gene such as exons, introns, promoters, Pribnow/Hogness boxes, etc. After structural annotation, functional annotation can be done by comparing the gene with a reference sequence and identifying similarities and differences between the two, thus enabling the identification of the function of specific regions on the DNA or specific genes.
ReplyDeleteI believe this process is especially important, because it enables researchers to understand how the advancement in bioinformatics technology is allowing them to not only identify and understand the function of genes, but actually be able to use it for improving human health. Thus, by understanding the function of genes, we can understand how new medicines can be created, from the knowledge gained from structural and functional annotation of an individual.
In my opinion Genomic Annotation is a process involving studying DNA and identifying the functional and in functional parts. It consists of three main parts, the nucleotide, protein, and process levels. Not all of the proteins in a genome have a function though, in fact it'd half of the predicted proteins don't. There are many gene finding methods but the most successful combines different ideas such as gene prediction and sequence comparison with expressed sequence databases. All of this is used for nucleotide annotation which allows the combination of genome sequences with other genetic traits of the genome. The genome must also be assigned functions to its products which is done by protein level annotations. Resources such as databases are useful for this type of annotation. Generally speaking, the main goal of process level annotation is understanding the function of genes and their context. Nonetheless it's a bumpy road and things such as inconsistency of the terms get in the way. From the video I found it interesting that so much experimenting has to be done just to learn a little information. Either way it's useful to know.
ReplyDeleteTo my understanding, genetic annotation is the process of finding the structural and functional information of genes and proteins. This can be used to identify the parts of a gene and connect them to their functions, which can be applied to real life medical scenarios. On the other hand, GWAS, or genome-wide association studies use data about SNPs to identify how differences in genetics can affect different people. These studies are typically done by using a computer program to analyze the effects of SNPs on a large population of people (ideally around 100,000).
ReplyDeleteI learned that a Genome-Wide Association Study is study of associations among genetic variations and a particular phenotype. DNA is made up of four nucleotides (A,T,G,C) which can code for variants based on their sequence at a certain location on the DNA. When a location on a DNA strand has different variants it is known as a Single Nucleotide Polymorphism (SNP), which allow for the causes for human traits to be explained (nurture or nature of traits). For the understanding of traits, association analysis is done, which uses a large sample of humans of the same ethnicity, then SNP locations are recorded and record the trait (genotype and phenotype). Association is computed with the use of software to remove faulty info and perform a regression analysis. The graph often has a slope when there is an association, stronger clustering along the line of best fit, the less chance for luck/chance and results in more reliability. Then a 0.05 threshold is used to check a null hypothesis, which is then divided by the number of snips to test significance, creating a Manhattan plot. These allow for the discovery of the association between genotypes and phenotypes and uncover biological causes that allow for the betterment of genetic treatments.
ReplyDeleteGenetic annotation helps find information about a gene's function. In Genome-Wide Association Study, regression analysis is performed on every SNP in a dataset, and each individual is a data point. The regression line would try to predict whether there is association between SNP and phenotype. Once a p-value is calculated for all SNPs, the threshold of 0.05 is divided by the number of SNPs, which reduces the number of SNPs that have an association with the phenotype. A Manhattan plot is then generated. Significant SNPs are often clustered together, and those are analyzed using SNP databases to indicate gene location, which helps uncover new biological mechanisms to prevent and treat genetic diseases.
ReplyDeleteGenetic Annotation is the process of finding the structural and functional details of a protein (or a gene). Genome-Wide Association Studies (GWAS) are used in the discovery of associations between certain variations in our genetic code (and a certain physical trait). GWAS is typically done using computer programs such as PLINK. With these programs, the "calculation" of millions of SNPs could take a few hours because of multi-threading . (Without them it could take days)
ReplyDeleteAfter the "calculations", a Manhattan plot is produced. Significant SNPs (the video uses the example of BMI) would be clustered together.
Genomic annotation is when researchers annotate genomes based on their function and structure. They locate what everything is in a genome, such as enhancers, promoters, repeats, and especially introns and exons. They also record what each part of the genes do, which is functional notation. I also learned from the video how data might be analyzed in a Genome-Wide Association study. After data is recorded from ideally around 100,000 people, it is put into a software to remove faulty information from individuals or snps. Then the information is graphed to try and locate connections between different factors in the data. A line is then drawn through the data to find a pattern. This is called a regression line. Then the p-value is calculated. The p-value is the chance that the distribution of data points was random or if there is a real correlation. I think that genomic annotation is probably very important because it literally explains what is going on in a genome. I also think it was interesting to see how researchers might discover correlations between two seemingly unrelated things through GWAs.
ReplyDelete- Annika Thakur, sorry I forgot to log in!
DeleteI find genomic annotation really interesting, and I think it is a very important aspect of bioinformatics. From what I understand, there are two main types of genomic annotation, structural and functional annotation. While structural annotation locates and labels the various genomic elements of DNA, such as introns, exons, and promoters, functional annotation is responsible for describing the functions and adding biological information to the structural components. I think genomic annotation is a crucial tool, and I really appreciate how it aids researchers in more efficiently analyzing DNA sequences. In addition, I really enjoyed the video's review of Manhattan plots, as we discussed in class.
ReplyDeleteI learned that genome annotation is the process of labeling and describing the various features of an organism's genome, such as genes and regulatory elements. Genome-wide association studies (GWAS) is a good tool for identifying genetic variants that are associated with particular traits or diseases, and can be done using genomic annotation. GWAS includes analyzing the DNA of large numbers of individuals to identify specific genetic variations that are more common in individuals with a particular trait or disease, compared to individuals without the trait or disease. Since genome annotations are important for providing information about the locations and functions of genes in the genome, it is easier for scientists to identify genes that are likely to be important for particular traits or diseases, and use GWAS to confirm whether these genes are indeed associated with the trait or disease. Furthermore, genome annotations can help to interpret the results of GWAS studies by providing information about the potential functions of the genetic variations that are identified. This can help to understand the underlying biological mechanisms that contribute to the trait or disease, and potentially lead to the development of new treatments. Overall, genome annotations and GWAS are important tools for understanding the genetic basis of complex traits and diseases.
ReplyDeleteGenetic annotation is used to identify the structure and function of a protein derived from a specific sequence in the genome. The specific sequence of nucleotides leads to a specific sequence of amino acids, making the structure and function of each protein unique. Using this knowledge, we can directly find the function of a specific chunk of DNA by tracing the path of protein synthesis and finding what protein is made. GWAS (genome wide association studies) processes are used to find genetic variants that can be traced to specific diseases or phenotypes. GWAS takes advantage of computer processing by using it to run tests on many SNPs at once to make the process more efficient.
ReplyDeleteThe information that I have gathered today is that gene annotation is an analytical and comparative process in which the structural and functional purpose of a gene or protein is derived from a raw data set. This process is highly important because it gives people valuable information about the genome or DNA and it can be used to predict genes or proteins that may come in a sequence.
ReplyDeleteGenome wide association study is the discovery of association of genetic variations to physical characteristics. In order to achieve this, the genome of a large group of people with similar origin must be collected, along with the respective physical characteristic we are attempting to link.
ReplyDeleteEvery SNP being studied is checked with the physical characteristic, looking for a possible relation.
This is only one of the forms of genetic annotation, which is functional annotation. Structural genetic annotation seeks to IDENTIFY where are the genes, functional annotation seeks to know what those genes do.
Structural annotation remains more linked to nucleotide-level, while functional works at a protein level.
Succesfully understanding what our genes do an where they are in our cells could allow us to identify genetic risk factors in diseases that could then be treated if we could modify those specific SNPs related to the risk factors.
Esther:
ReplyDeleteBefore the GWAS, the model for studying many diseases was the family lineage, and because consanguineous marriages were so common, a royal family member often suffered from hemophilia. But hemophilia is a disease that is very small, or very common in one family, in one network. How do you study more common, more common diseases in larger populations, even populations that are not related to each other? GWAS came along, and it was able to analyze a lot of the data that was collected. To find out which locus of genetic mutation or SNP is associated with disease or trait (trait). That's where GWAS come in.
In simple terms, genomic annotation is trying to figure out and label a complete genome. From the class I learned that we need to put multiple reads together in contigs to assemble a complete genome using a reference genome. First the locations of genes and other details are identified along with what they do, then biological elements are added to those locations. Hence there are two types of annotation: structural and functional.
ReplyDeleteGenomic annotation allows researchers and other people to see genetic data in a more purpose full way. Structural annotation tells us about the structure of the gene, the introns, exons, etc. Functional annotation tells us what is the function of the gene, what proteins it can code for etc.
ReplyDeleteBrady
DeleteGenomic annotation is a multi-level process in which we need to predict different codes of genes and to identify the functional elements within a genome sequence. It is very analytical and it helps find out what elements are on the genome. Location of genes are found and there are two types of annotation.
ReplyDeleteAllison Oh
Genomic annotation is the process of locating genes and coding regions to determine the gene's function, named structural annotation. It also labels all elements inside of a gene based on its individual parts, which is called functional annotation. To annotate genomes, you first need to have the full genomic sequence from websites such as NCBI. Then you can use servers like Prokka to automatically get the annotation that you need.
ReplyDeleteGenomic annotation is essentially a multi-level process with the goal of identifying the elements in a genome. With this information, we can figure out what these elements, such as genes, can do. There are two types of genomic annotation, structural and functional annotation. Structural annotation identifies important elements of DNA while function annotation describes the functions of these elements as well as adds biological information to them.
ReplyDeleteI found it interesting how 99.9% of humans genetics are the same. I learned that a SNP is not a mutation but a genetic variant that gives humans their diversity. I learned how SNPs can be heritable. SNPs give humans their traits and traits can come from our environment. I found that interesting. So does this mean you can alter your DNA? I also learned that GWAS can help us understand what biological mechanisms in our body might be affecting our traits. A software named PLINK can help run GWAS testing.
ReplyDeleteGenomic annotation is the process of identifying the locations of genes and the coding regions in a genome to determine the purpose of those genes. This process can be categorized into structural annotation and functional annotation. Structural annotation involves the identification of genetic elements such as coding regions, locations of regulatory motifs and gene structure. Functional annotation involves the attachment of biological elements to locations on the genome. Examples of the type of information that may be included are biochemical function, involved regulations, and biological function.
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