Genome Browser Tutorial Level 1

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Welcome to Genome Browser! This overview is meant to introduce you to a few of the basics of this tool. We’ll go through the process of looking up a gene, finding the databased information about that gene (including the sequence), and locating chromosomal elements around the gene such as CpG islands and chromatin modifications. This tutorial works well if you have a simple gene to search for alongside your reading of the tutorial.  If you’re looking for a more basic introduction to what this tool actually is and what information it contains, check out “Genome Browser Tutorial Level 0”.

If you’re using UCSC Genome Browser, this is the first page you will see when you pull it up on google. Notice there are several different tools, one of which is Genome Browser. Along the column on the side, you’ll see Genome Browser and Blat (Basic Local Alignment Tool). Genome Browser is useful for searching for a gene name or a chromatin locus (when you have the numerical position of the area you’re searching). Blat is useful when you have a sequence and would like to locate it in the genome.

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If you click on Genome Browser on the side column, the page below will be the first to appear. The “Genome Browser” link along the top tool bar will shortcut you to a scalable view of the genome. We’ll get to that later.

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While the default is set to the human genome, you can choose other species.

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Be aware also that due to the nature of genome sequencing, there are different versions you can search under the “assembly” list. If you’re having trouble locating a region someone else has referenced, they may be using a different assembly than you are. Feb 2009 tends to be the default assembly.

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If we know what gene we want to search, we can enter it’s name in the “search term” box.

Here, we’ll look for corticotropin releasing hormone (CRH). Genome browser will suggest several search terms–choose the one that best fits you or type in exactly what you’re looking for.

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Once we hit “submit”, a scalable view of the chromosome along the gene you’ve searched will appear. This is also the scalable view you will see if you click on the “Genome Browser” link at the top toolbar (this link takes you straight to this view without allowing you to specify the gene for which you are looking).

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If you were to search “CRH” alone, without selecting the more specific option Genome Browser suggests, you might see this page appear. Don’t panic… Just choose whatever seems to best fit what you’re looking for. In this case, it is the first option on the list.

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If we return to the scalable view, we can work on simplifying what we’re looking at.

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Right clicking on elements in the center (look for the text descriptions in black and circled in red) will make the list below appear. Click on “hide” to hide single elements in a section.

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Alternatively, we can work with whole sections at once. Hover over over a grey bar on the side to highlight the section you’d like to manipulate. You can drag this section to reorder or right click to configure or hide the section.

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When you right click, this menu should pop up.

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Click “hide track set” to make the entire section disappear. Don’t worry! You can get it back later.

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We can also zoom in or out, showing more or less detail using these buttons:

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If you wish to drag to reorder rather than hide, click, hold, and drag the grey bar on the left side. Here we’ll move “CpG Islands” below “H3K27ac Mark”.

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Ta Da!

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If you use your cursor to highlight a section of the gene, this dialogue box will appear:

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This allows you to zoom in to the section you’ve highlighted or to overlay color onto the section highlighted, effectively HIGHLIGHTING it.

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We can add items to the visual window by scrolling down to the various menus and selecting new information. If I wish to show the CpG islands on the gene, I would select “show”, “pack”, “dense” etc to display them. Each of these options will show a different amount of information in the space, spreading it out or condensing it. “Hide” will remove this information from the visual window.

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An example of the menu under each of these blocks of information is displayed here. The “Ensembl Genes” feature shows genes annotated on the chromosome within another genome browser called “Ensembl”.

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Let’s return to the visual window. If you click on the gene name to the far left (highlighted in black), a descriptive page will appear.

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This page describes the gene, its function, position, sequence, protein structure, expression patterns, and other information.

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Scroll down the page to find the predicted protein domains and structure. Not all genes encode proteins, and not all identified protein-encoding genes have a predicted 3-D structure, but some do. Available information may vary between different genes.

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Also on the main information page for the gene, we can also see the relative gene expression levels in different tissues. Remember, this data will be specific to the species you selected when you started your gene search. Usually, the default expression setting will be Red = high expression and Green = low expression.

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If you wish, you can change this color scheme to Yellow= high expression and blue = low expression.

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If you wish to get the genomic and flanking sequences for your region of interest, you can go to the “Sequence and Links to Tools and Databases” section and click on “Genomic Sequence” (circled in red).

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When you click on this, you will have an opportunity to specify the parts of the sequence in which you are interested.  Here, you can request the sequences outside of the gene.

These include:

“Promoter/Upstream”– sequences upstream of the gene’s transcription start site (TSS);
“5′ UTR Exons–the upstream 5′ untranslated region (UTR), i.e. not translated to protein;
“3′ UTR Exons”–the downstream 3′ regions not translated  to protein;
“Downstream by”–the sequences beyond the end of the gene’s exons.

Within the gene, selecting the “CDS Exons” will give you the coding sequence exons. If you select no other boxes, this will give you only those exons that encode protein (just like cDNA–coding DNA). Selecting “Introns” will give you the noncoding gene introns between the coding exons. Be careful–if your gene has alternative splicing, exons may be used in some versions of the transcript but not in others.

You can also use formatting options to distinguish between different gene sections. Select the boxes under “Sequence Formatting Options” to specify these settings.

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Once you submit your request, the sequence will appear in this format:

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Got the basics yet? If you have more questions, feel free to email us (Kira specifically) to request clarification or a walkthrough of other Genome Browser functions. Good luck!

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3 Comments Add yours

  1. I really appreciate your post and you explain each and every point very well.Thanks for sharing this information.And I’ll love to read your next post too.

    Like

  2. krienecker says:

    Great! So glad it’s been helpful. We welcome suggestions for new topics.

    Like

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