This article describes a method on finding tissue-specific gene expression information for organisms that have records in the Gene database. If you are working with human, mouse, or rat genes see the article on using the Gene Expression display.
- Locate the gene of interest in the Gene database (example).
- Go to the Sequence Viewer tool in the Genomic regions, transcripts, and products section of the record.
- Click the Tracks button and select Configure Tracks to access the Configure Page.
- Select Expression as your track group to load tracks from a set of RNA-Seq studies that include:
- two tracks (one of these is for unique hits only*) that aggregate exon coverage for all included RNA-Seq reads
- two tracks (one for unique hits) that aggregate intron-spanning** reads
- numerous exon coverage tracks for individual tissues (may also include developmental stages)
- numerous tracks for intron-spanning reads
- Select the track(s) of interest and click Configure to add the tracks to the display.
- Use the Search Tracks button that is located on the left side of Configure Page to locate individual tracks. Enter a search term relating to a tissue (for example: fat) or a sample accession from an included study (for example: SAMN04019672)
- Check the NCBI Recommended Track Sets in case they include tracks of your interest (For visual instructions see the YouTube video on using the Recommended Track Sets.)
- Once you have your tracks added, use the Tracks button to save your selection as a My NCBI Track Collection (as shown in the My NCBI Track Collection video) for your future work.
Use these tips to adjust the tracks/analysis to your needs:
- To choose between linear and logarithmic scales hover over a individual track description. In the pop-up text window, select the Track Settings (the gear icon).
- Uncheck the tracks that you do not want (for example the aggregate tracks) by clicking on the red X symbol located on the right side of each individual track.
- You may find comparison more convenient if you zoom in on a certain range of the gene rather than viewing the entire gene.
- Note that the Genome Data Viewer (accessible through the Genome Browsers link located on the right side of a Gene record; example) also provides expression tracks. Manipulating tracks in the Genome Data Viewer works similarly to that in the Sequence Viewer.
*Unique hits are those RNA-Seq reads that align to a single genomic location
**An intron-spanning read is an RNA read that originates from a single region of a transcript but it maps to two locations on the genome indicating the splice junction of two exons in the transcript. Think of the blue intron blocks that you see in the graphics as a fusion of numerous lines that are connecting the split-mapped reads from the end of one exon to the beginning of the neighboring exon on the genomic sequence. The NCBI Eukaryotic Genome Annotation Pipeline uses the intron-spanning reads as evidence for splicing (splice variants), but they can be used as a measure for relative gene expression.