Isoform expression profile view in genome browser

From Array Suite Wiki

Jump to: navigation, search

Contents

Isoform Expression Profile View in Genome Browser

In ArraySuite, transcript/isoform expression can be quantified by Report Gene/Transcript Counts function, which is based on a gene model, such as RefGene.

Some transcripts/isoforms are differentially expressed in different tissue/diseases. Once a differentially expressed isoform is detected by Differentially Expressed Isoforms detection function, a lot of users are interested in verifying it in genome browser visually.

OmicSoft Genome Browser provides a color scheme to represent the isoform differential expression. Here is one example on two samples, hESC and N2, where transcript uc001sjx.2 is primary expressed in hESC and uc001sjw.2 is primary expressed in N2:

20130410 isoform.png

Generate .ngs2tex files

When you run the Quantify Gene/Transcript Counts module, a set of .ngs2tex files will be generated.

  • Copy these files to the same folder as the .bam files you want to display in the Genome Browser.
  • Make a note of the Gene Model used to quantify transcripts; this model must match the gene model displayed in the Genome Browser.

Set up the Genome Browser

  • Make sure that the Gene Model matching your quantification is one of the tracks in the Genome Browser.
  • Right-click the gene model track, and select Set Track Properties
  • Set Show Transcript Quantification to True

Interpret the Transcript Display

  • Each sample will be assigned with one color (e.g. red for hESC and purple for N2)
  • The Genome Browser dynamically calculates the expression percentage, ranks the transcripts, and paint colored stack bars on transcript
    • Highest expressed isoform (based on the total expression from all samples) is on the top
    • The stack bar height or the color filling area represents the percentage of expression from corresponding sample/group
    • Low expressed isoforms are faded (transparency is calculated based on the transcript expression from all samples)

In the example above, uc001sjx.2 is primary expressed in hESC (mostly in red) and uc001sjw.2 is primary expressed in N2 (mostly in purple).

  • When you mouse over, it will show the expression percentage for each transcript in each sample:
    • For the same gene, get the total expression (GTT) = sum of expression values from all transcripts in all samples
    • The expression percentage from each transcript in each sample = transcript expression in the sample / GTT

20130410 isoform2.png

Turn off the visualization by an option in the track property:

20130413 TurnOffTxn.png

Video Demonstration