Expression tracks

Both tracks can be shown in a Table (Image table) and a Graphical (Image annotation_track_16_n_p) view.

The expression track table view has the following options (figure 28.12).

Image mrna_seq_result_table
Figure 28.12: RNA-Seq results shown in a table view.

By creating a Track list, the graphical view can be shown together with the read mapping track and tracks from other samples:

        File | New | Track List (Image trackset_16_n_p)

Select the mapping and expression tracks of the samples you wish to visualize together and select the annotation tracks used as reference for the RNA-Seq and click Finish.

Once the track list is shown, double-click the label of the expression track to show it in a table view.

Clicking a row in the table makes the track list view jump to that location, allowing for quick inspection of interesting parts of the RNA-Seq read mapping (see an example in figure 28.13).

Image mrna_seq_result_contig
Figure 28.13: RNA-Seq results shown in a split view with an expression track at the bottom and a track list with read mappings of two samples at the top.

Reads spanning two exons are shown with a dashed line between each end as shown in figure 28.13, and the thin solid line represents the connection between two reads in a pair.

When doing comparative analysis, double click on one of the Expression or Statistical Comparison tracks in a track list to get its table view. Then click on the "Select genes in other views" button in any other table or expression browser will cause the track list to zoom to the selected gene.

Expression tracks can also be used to annotate variants using the Annotate with Overlap Information tool. Select the variant track as input and annotate with the expression track. For variants inside genes or transcripts, information will be added about expression (counts, expression value etc) from the gene or transcript in the expression track. Read more about the annotation tool in Annotate with Overlap Information.

Gene-level expression

The gene-level expression track (GE) holds information about counts and expression values for each gene. It can be opened in a Table view (Image table) allowing sorting and filtering on all the information in the track (see figure 28.14 for an example subset of an expression track).

Image mrna_seq_result
Figure 28.14: A subset of a result of an RNA-Seq analysis on the gene level. Not all columns are shown in this figure

Each row in the table corresponds to a gene (or reference sequence, if the One reference sequence per transcript option was used). The corresponding counts and other information is shown for each gene:

Transcript-level expression

If the "Genome annotated with genes and transcripts" option is selected in figure 28.4, a transcript-level expression track (TE) is also generated.

The track can be opened in a Table view (Image table) allowing sorting and filtering on all the information in the track. Each row in the table corresponds to an mRNA annotation in the mRNA track used as reference.

Additional information to GE or TE tracks

Both GE and TE tables can offer additional information such as hyperlinks to various databases (e.g., ENSEMBL, HGNC (HUGO Gene Nomenclature Committee), RefSeq, GeneID, etc.) In cases where the mRNA track or the gene track provided have biotype information, a biotype column will be added to the table.