NCBI Gene: Expression

Open https://www.ncbi.nlm.nih.gov/gene

in another browser window to work through this tutorial side by side.

NOTE: Use the Single-page view to do this lesson or the database Sort may not work properly.

Single-page view

NCBI Gene is a portal to gene-centered information from different sources.

This tutorial shows how to answer the question:

In what tissues and under what conditions is the gene expressed?

Click next for an example scenario.

Topic 1: Finding Gene Expression in Normal Tissue

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Example: In what normal tissues is the mitochondrial transporter SLC25A3 expressed?

In the Gene database, search for human SLC25A3 by entering:

SLC25A3[symbol] AND human[orgn]

Topic 1: Finding Gene Expression in Normal Tissue

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This search takes you directly to the record for the human SCL25A3 gene.

We're looking for information on expression of the gene in different normal tissues.

Use the Table of Contents to jump to the Expression section of the record.

Topic 1: Finding Gene Expression in Normal Tissue

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expression histogram

  • The histogram graph shows counts of next-gen RNA sequences from samples of human tissues aligned to the genome in the region containing this gene.
  • The units (reads per kilobase per million reads placed = RPKM) are normalized to give relative expression numbers that can be compared.

According to this histogram, in what tissue is the mitochondrial transporter SLC25A3 most expressed?

Topic 1: Finding Gene Expression in Normal Tissue

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Click on the See details link.
 
details link
 
This will show more information and a table of values.
 
There are datasets from several different studies available in the NCBI databases. Different studies may have data on different tissues.
 
The default study is the Human Protein Atlas. Note the label, "HPA RNA-seq normal tissues." 
hpa study description
HPA stands for Human Protein Atlas. This dataset shows expression in a number of places in the body but especially heart.
 

Does this Human Protein Atlas dataset include expression data for skeletal muscle?

 

Topic 1: Finding Gene Expression in Normal Tissue

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Let's look at a different dataset.

Select the "RNA sequencing of total RNA from 20 human tissues" set.
expression dataset options
 
Note that a different list of tissue samples is displayed in the histogram.
 
This set also shows high expression of SLC25A3 for heart. Note that the "RNA sequencing of total RNA from 20 human tissues" dataset includes skeletal muscle, which was not present in the HPA study.
 
Go back to the full Gene record for SLC25A3 to continue to the next topic.

Topic 2: Finding Changes in Expression Using Microarrays

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Example: Are there any microarray experiments that show changes in the expression of this SLC25A3 gene?

Microarray studies measure the abundance of particular RNA species through the extent of binding to complementary probes on a chip. The profiles show the abundance of mRNA for a particular gene across all samples in the experiment. Experiments can include time courses after treatment with an agent, varying developmental stages, tumor vs. normal tissues, comparisons of various tissues or cell lines.

NCBI-curated microarray studies are available through the GEO profiles link in the right-hand Related information column in the NCBI Gene record.

Geo Profiles link in sidebar

To use these data you really need to know what experiment you are interested in.

Follow the link to GEO profiles from the Related Information section of the human SLC25A3 Gene record.

Topic 2: Finding Changes in Expression Using Microarrays

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We're now looking at data extracted from microarray experiments, where the experiment tested for expression of the gene SLC25A3. Each result represents a gene expression profile: a group of data from an experiment that may reveal something about how the gene is expressed in a particular condition.

One useful way of sorting these results is by "Subgroup effect."

Subgroup effect sort

This brings to the top the experimental data where expression was most notable.

Scroll through the results until you find "Muscle function and aging - female (HG-U133A)." This is one of several microarray profiles showing a decline in expression of this gene with aging.

(Again, you probably need to have an idea of what you are looking for in this data, so this is just an interesting example for illustration.)

Topic 2: Finding Changes in Expression Using Microarrays

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Click on the thumbnail of the histogram, to the right of the description, to view the relevant data from this dataset.

GEO results example

Topic 2: Finding Changes in Expression Using Microarrays

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We're now viewing one "profile:" Data extracted from the results of one experiment, showing how this particular gene was expressed.

geo profile

You can click around this viewer to learn more about this experiment.

What does each data point in the histogram for this GEO profile represent?

 Return to your GEO Profiles results.

Topic 2: Finding Changes in Expression Using Microarrays

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We've now explored a relevant gene expression profile from one experiment. Let's look at the GEO Dataset record for this same experiment (GDS472). Find the "Muscle function and aging - female (HG-U133A)" result, again.

Then:

Click GEO DataSets:

link to GEO Datasets

and click "Muscle function and aging - female (HG-U133A)":

link to dataset

Topic 2: Finding Changes in Expression Using Microarrays

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We're now in the GEO DataSet Browser, looking at the record for DataSet GDS472: a study comparing gene expression in skeletal muscle in young vs. older women. We were looking at specific data on SLC25A3 expression from this study a moment ago. Now we're looking at information about the dataset as a whole.

The Data Analysis Tools in the lower half of the screen allow you to compare the samples and look at genes that are "up" or "down" for the condition(s) studied. For this particular dataset, the condition of interest is age.

Please return to the Gene record for SLC25A3 to continue.

Topic 3: Finding Tissue-Specific Expression of Splice Variants

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Example: This transporter has different splice variants. How can I see whether any of these have tissue-specific expression patterns?

To find tissue-specific expression of splice variants, we will go back to the RNA-seq data, linked from the Gene database record.

Scroll to the embedded Graphical Sequence Viewer display (in the "Genomic regions, transcripts, and products" section).

graphical sequence viewer

The display shows the genomic sequence at the top with the aligned mRNA products (transcripts) immediately below:

3 transcripts

The mRNAs align only to the portions of the gene (exons) that are spliced together to make the transcript.

This gene has three different mRNA sequences (transcript variants or splice variants) as shown in the graphic with different patterns of exons.

Topic 3: Finding Tissue-Specific Expression of Splice Variants

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Notice at the bottom of the viewer that the next-gen RNA data (RNA-seq intron features, aggregate (filtered)) are shown as a histogram chart across the gene.

RNA-seq data

These data highlight the expressed portions of the gene, the exons -- those that are spliced together to make the messenger RNA.

The track that best shows the pattern of exons is the intron-spanning reads track, which provides a negative image of the exons.

Topic 3: Finding Tissue-Specific Expression of Splice Variants

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You can add an entire set of these tracks for different tissues. This is useful because in some cases particular splice variants have tissue-specific expression.

Click on the "Tracks" menu (the gear icon) in the viewer and select "NCBI Recommended Track Sets," "Expression."

configure tracks menu

This data is from the expression studies that we looked at in the Expression histogram, earlier.

Topic 3: Finding Tissue-Specific Expression of Splice Variants

4 of 4Once you open the Expression tracks, you will need to re-expand the transcript tracks, to see differences between the splice variants.

Click SLC25A3 (+6) at the very top of the graphical sequence viewer:

slc25a3 +6

Notice that there is a particular exon that appears in one of the splice variants (NM_005888.3).

NM_005888.3

Now if you look at the the location of the exon and find the same locations on the expression tracks, below, you can see where different tissues preferentially express the gene.

For example, look at the heart track:

comparing tracks

(Note that, for purposes of illustration, we've removed a number of tracks for this screenshot. You will need to scroll or remove tracks to find the track that reads, "RNA-seq intron-spanning reads, adult, heart...")

What is special about the splice variant NM_005888.3?

Summary

You have reached the end of the tutorial for the question: In what tissues and under what conditions is the gene expressed??

NCBI Gene Help Resources 

Continue to Chapter 11. What are the equivalent genes (homologs) in other species?

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