Using the UCSC Genome Browser

UCSC Genome Browser: https://genome.ucsc.edu/

Open the UCSC Genome Browser from the link in this document or from the Exercise 1 homepage.

Beneath the headers is a dark blue bar with the link “Genomes.” Hover over it and select the human genome GRCh38/hg38. Alternatively, click the link, and it will open a search window for the latest Human assembly as the default option.

Type “TP53” into the search text box, and it will list many possible matches. Select the second one, which corresponds to tumor protein p53 (from HGNC TP53).

The gene size and coordinates of where this gene falls on Chr 17 should be very similar, if not identical, to the coordinates listed for the NCBI gene record.

Scroll down through the graphics. Clicking on the graphic or the name of the track will pop open a window with information about the track. Click on any single transcript to see details about the transcript.

The instructions you provided are for using the UCSC Genome Browser to search for the TP53 gene and view its genomic location and associated details. Here’s a step-by-step guide to complete the tasks:

1. Open the UCSC Genome Browser: Go to the UCSC Genome Browser website at https://genome.ucsc.edu/.
2. Select the Human Genome (GRCh38/hg38):
   • Below the headers, you will find a dark blue bar with the “Genomes” link. Mouse over it.
   • A menu will appear. Click on “Human.”
3. Search for TP53:
   • Once you have selected the Human Genome, you’ll see a search text box on the top right.
   • Type “TP53” into the search text box and press Enter.
4. Select the TP53 Gene:
   • The search results will list possible matches for “TP53.”
   • Select the second one, which corresponds to “tumor protein p53 (from HGNC TP53).”
5. Explore Gene Location and Details:
   • After selecting the TP53 gene, you will be directed to a page showing its genomic location on chromosome 17.
   • Scroll down through the graphics to view additional information.
   • You can click on the graphic representing the gene or click on the name of the track to access detailed information about the track.
   • To see details about individual transcripts, click on any single transcript within the track.

By following these steps, you can use the UCSC Genome Browser to search for the TP53 gene, visualize its genomic location, and access information about its transcripts and associated details. The UCSC Genome Browser is a powerful tool for exploring and analyzing genomic data.

Indeed, a genome browser is a valuable tool for addressing a variety of questions related to genomic data. Here are answers to your questions:

1. What genes are located near it or may share promoters?
   • You can use the genome browser to view neighboring genes and their genomic locations relative to your gene of interest. This information can help identify nearby genes that may share regulatory elements or promoters with your gene.
2. What SNPs are found in my gene, and are they located in introns, promoters, or exons?
   • Genome browsers often include tracks with information about Single Nucleotide Polymorphisms (SNPs). You can visualize the locations of SNPs within your gene and determine whether they are located in introns, promoters, exons, or other regions. This information is crucial for understanding genetic variations within the gene.
3. What strand is my gene encoded on?
   • The genome browser provides information about the strand on which your gene is encoded. This is essential for understanding the orientation of the gene and its exons and introns.
4. What regulatory elements are located within or near my gene?
   • Genome browsers often include tracks for regulatory elements such as enhancers, promoters, and transcription factor binding sites. You can identify these elements within or near your gene, providing insights into its regulation.
5. What clinical variants are associated with my gene?
   • Many genome browsers incorporate tracks with information about clinical variants, disease-associated mutations, and other relevant data. You can use this information to explore the clinical significance of variations within your gene.

Genome browsers are versatile tools that enable researchers to explore a wide range of genomic data, helping to answer specific questions and gain insights into gene regulation, variations, and associations with diseases or clinical conditions.

A relatively new default track at UCSC is the gene expression data in different tissues from the NIH Genotype-Tissue Expression (GTEx) project. This project was created to establish a sample and data resource for studies on the relationship between genetic variation and gene expression in multiple human tissues. This track displays median gene expression levels in 54 tissues and 2 cell lines, based on RNA-seq data from the V8 GTEx data release (October 2019). This release includes data from 17,382 tissue samples obtained from 948 adult post-mortem individuals.

6. What is the conservation of my gene’s sequence across species?
   • Genome browsers often provide the ability to view the conservation of a gene’s sequence across different species. This information can help assess the evolutionary significance and functional conservation of the gene.
7. Are there known microRNA binding sites in the 3′ UTR of my gene?
   • You can investigate whether there are microRNA binding sites in the 3′ untranslated region (UTR) of your gene. MicroRNA binding can play a crucial role in post-transcriptional regulation.
8. What is the gene’s expression pattern in different tissues or under various conditions?
   • Many genome browsers include transcriptomics data that show the gene’s expression in different tissues or conditions. This can help you understand when and where the gene is active.
9. What is the epigenetic landscape of my gene, including DNA methylation and histone modifications?
   • Epigenetic data tracks in the genome browser can provide insights into DNA methylation patterns and histone modifications within and around your gene. This information can indicate the gene’s regulatory state.
10. What is the genomic context of my gene, such as neighboring elements, repeat sequences, or structural variants?
    • You can explore the genomic context of your gene, including the presence of transposable elements, repeat sequences, and structural variants that may influence its function or regulation.
11. What are the nearest neighboring genes on both sides of my gene, and what are their functions?
    • Identifying the nearest neighboring genes and understanding their functions can provide insights into potential gene clusters or co-regulation patterns.
12. What pathways or Gene Ontology terms are associated with my gene?
    • Genome browsers may provide information about pathways or Gene Ontology terms associated with your gene, helping you understand its biological functions and potential roles in specific processes.

These are just a few examples of the questions that can be addressed using a genome browser. Depending on the genome and available data tracks, you can investigate a wide range of genomic and functional aspects of a gene or genomic region, making genome browsers essential tools for genomics and bioinformatics research.