NCBI Gene: Expression (Part 1): Finding Gene Expression

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.

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]

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.

• 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.

Click on the See 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 stands for Human Protein Atlas. This dataset shows expression in a number of places in the body but especially heart.

Let's look at a different dataset.

Select the "RNA sequencing of total RNA from 20 human tissues" set.

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.

You've completed this tutorial. Close both windows to end the Guide.