Search box on library’s website will be on top right of every page

In an effort to continually improve your web experience, we’re rolling out the following new features this month:

  1. We’re moving the search box to the top right area of the header
    • The search box will be available on every page (not just the homepage)
    • We will meet users’ general expectations for the search box to be located in the top right of the page
  2. We’re adopting the new look of the CU Anschutz Medical Campus website in order to:
    • Create a more fluid user experience
    • Help promote a more consistent look and feel across university websites
    • Support CU’s larger marketing and branding initiatives

Test drive the search box (link will only work on campus)
Tell us what you think

HSL-homepage-new-features

We look forward to your comments on our new look!

For questions, please contact:
Vivienne Houghton, MLIS
Web Services Librarian
303-724-2178
vivienne.houghton@ucdenver.edu

Thank you!

WEBwwg

BoardVitals Trial

Image

The BoardVitals trial (through STAT!Ref) is from July 6th-26th, 2015.

To access the trial: Go to the BoardVitals trial page and follow the registration instructions.
Tell Us what you think!

Featured in our BoardVitals trial are question banks for:

18 Medical Specialties
Shelf Exams
USMLE Step 1
USMLE Step 2
USMLE Step 3
NBDE I
NBDE II
NAPLEX
NCLEX RN
NCLEX PN
Family NP
COMLEX
PANCE
Surgical Tech

More about BoardVitals

Bioinformatics Bite: How to find the transcription start site of a gene.

Today’s bioinformatics bite is the patron question we’ve been leading up to in previous posts:

How do I find the transcription start site of the human signal transducer and activator of transcription 1 gene?

Step 1: Find the official gene name:

STAT1

Step 2: Search the gene database using the gene name and organism tags

STAT1[Gene Name] AND human[Organism]

Step 3: Profit. And by profit I mean find the transcription start site using this gene’s entry in the gene database. Here’s what the gene page after running the search above.

STAT1 gene page (click to enlarge)

The top left shows basic information about the gene, like the Gene ID (6772), which is the unique identifier for this gene. Also, there’s an entry in the summary section for Orthologs, which links to the Gene entries for STAT1 in other organisms. But let’s get back to the original question.

Notice the Table of Contents in the right column. The links in this section let you jump to your section of interest on the Gene page, which is especially useful because there is A LOT of information contained in these pages.

Click on Genomic regions, transcripts, and products.

GenTxPdt

This brings up the Genome Browser. The dark gray bar near the top of the browser represents the genome and is marked with base pair positions. The green lines represent Transcripts. The red lines represent Coding Regions. There are two sets of transcripts here: those modeled by NCBI on the top, and those modeled by Ensembl at the bottom. They use prediction algorithms, so discrepancies are normal.

Let’s zoom in a bit on the 5′ end of the STAT 1 transcript to get a better look. (You can approximate the region i’m looking at using the genome position bar at the top.)

transcript zoom

First, let’s talk about the difference between the transcripts and the coding regions. Coding regions only contain the protein coding parts of the transcript. They do not include the untranslated regions (UTRs), so I wouldn’t look here for the 5′ end of the transcript.

Transcripts contain the entire sequence that is thought to be transcribed. The thick green boxes represent the exons, and the thin green lines represent the introns. Some of the exons are dark green, indicating that they are coding exons. The light green exons are noncoding exons. Isn’t it nice that the coding exons line up with the coding region?

Next, look at the three transcripts. Notice that 2 of them are labeled with a number that starts with NM_ and the other one is labeled with XM_. These numbers are their accession numbers, which is the unique identifier for a nucleotide sequence. The ones that start with NM_ are backed up by experimental data, probably RNA-seq, and the XM_ ones are predictions based on sequence alone. If you mouse over the accession number, it will give you basic information about the transcript, including the accession number of the protein that it encodes (the NP_ number).

transcript mouseover

Now let’s get down to business answering the question! Scroll back to the top of the gene page and click the arrow next to display settings and select Gene Table.

Display gene table

This brings you to a pretty similar view of the transcripts in the genome browser, while adding a feature called Exon table at the bottom.

Gene table

Click the plus sign to the left of one of the transcripts (preferable a NM_ transcript) to see the table.

transcription start

This table contains the genomic positions of all of the exons in the chosen transcript, while indicating the coding parts. If you want to know the transcription start site, look at where the first Exon starts.  Note that this gene is on the negative strand so the number ranges are backward. The genome browser flipped it around for you automatically.

Finally, note which chromosome in the Genomic Context section.

genomic context

You can also export the exon table by selecting Send to: File at the top of the page and selecting Gene Table (text) from the dropdown menu.

send to

Thanks for reading! Hope that everyone has a nice Fourth of July holiday!

– Tobin Magle, Biomedical Sciences Research Support Specialist

Bioinformatics Bite: Searching the gene database

This bioinformatics bite is another basic skill needed to answer another patron question: how to effectively search the gene database. Last week, I showed you how to find official gene symbol. We’re going to look for the gene entry for human signal transducer and activator of transcription 1, or STAT1.

Let’s start at the gene database main page. Try entering STAT1 into the search box. This query returns over 800 gene results, but we’re looking for one specific gene. Not super efficient.  Let’s take a second to explore the results page though.

stat1gene page

The left hand column contains filters. For example, if you’re only interested in protein coding genes, you can apply that filter and get rid of noncoding genes. You can see what filters are currently applied by looking at which are checked in the left column.

The only filter that is applied right now is “Current Only” under status. The restricts the results to only gene predictions that are, well, current. NCBI is always updating Gene entries based on new experimental evidence, so some entries become obsolete, but you can still see the old entries by clicking ” See also 2 discontinued or replaced items” above the results box.

Next, let’s look at the results column in more detail:

STAT1 human

The first name is the official gene name and the Gene ID. The Gene ID is the unique identifier for this gene in the NCBI gene database. If I wanted to pull up STAT1, and i knew its gene ID, I could type it into the search box and it would come up right away.

The second column is the Description, which gives the spelled out name of the gene, sometimes an indication of its function, and the organism that it is found in.

The third column is the Location, or the Chromosome and bp where the gene is found.

The fourth column contains Aliases, or other names by which this gene is known. This field is helpful if a gene name has changed and you know the old name but not the new name.

Finally, the fifth column contains the MIM identifier, which is the unique identifier for this gene in the Online Mendelian Inheritance in Man (OMIM) database, which is a catalog of human genes and genetic disorders. Looking the gene up in OMIM gives you information about what phenotypes can occur when there are alterations in this gene, as well as a host of information about how the gene was cloned, its structure, and it’s function. This is a good place to start when studying a new gene.

The right hand column contains yet more filters. You can change what appears there by clicking “Manage Filters”.

right side filters

Below filters, you can see your results divided up by taxon. Right now, it’s displaying Top Organisms, which works because we are looking for a human gene. If you need a gene from a more obscure organism, click “Tree” at the top or “More” at the bottom.

results by taxon

Do you really think there are over 300 STAT1 genes in humans? Probably not. Let’s click that number to see what’s going on.

stat 1 human results

Scrolling down the list, you can see that they are all indeed human genes, but only the first one appears to be called STAT1. Why are all these other genes coming up? There’s a clue in the search details box:

human search details

See where is says “stat1[All Fields]”? This means that if STAT1 comes up ANYWHERE in the gene record, it will be retrieved by this search. How do you prevent this? Instead of letting it search all fields, specify that it should search gene name only:

STAT1[Gene Name]

When you search this query, the number of entries goes down dramatically, and you can see by looking at results by taxon, only one human gene appears. You can get to it by clicking on the number.

Now that you understand a little better how the gene database works, how would you get to the human STAT1 gene in 1 query? Combine the gene query with the organism query:

STAT1[Gene Name] AND human[Organism]

Type that in the search box, and it’ll take you right to the gene page.

Next time we’ll dig into the content on the gene page.

New Exhibit – Michael Keyes: Stories & Seasons in Woodcut

"Sunny Morning" woodcut print by Michael Keyes

The Health Sciences Library will be hosting an exhibit of woodcut prints by Aurora artist Michael Keyes from July 1st – August 31st. Stories & Seasons in Woodcut will be on display in the 3rd floor Gallery.

Woodcut prints are a type of relief printing. The prints are created when an artist cuts a picture into a wood block, then puts ink on the block and presses it to paper.

Michael Keyes will be hosting an Opening Reception on August 7th from 2:00 – 5:00 pm. Stop by during that time to meet Michael and ask him about woodcutting.

The Gallery is accessible during the library’s public access hours.