Tutorial 3: Visualizing Gene Annotations

When you start this page, you should have downloaded your genome database. If the database you downloaded ends with “.gz” or “.zip”, you need to unzip it using gzip, unzip, WinZip, WinRAR or other software. If the database you downloaded ends with “.exe”, you just need to double click it to install, since this is a self-extractable file.

 

With the genome database available, you can add gene annotations to your track. You can either add them automatically or you can add them manually.

 

1. Add Gene Annotations Automatically

When you analyze your ChIP-seq data, you have already loaded the genome database into CisGenome. If nothing wrong, after you run peak detection, you should already have a CisGenome Browser session in which read signals are displayed side-by-side with gene structures, cross-species conservation and DNA sequences.

2. Add Gene Annotations Manually

You can also load gene structures, cross-species conservation and DNA sequences manually into your browser session. This is very useful when you want to display data processed previously or processed by other software.

In order to add gene annotation information manually, first click “add track” button (red circle 1) on your browser page.

A new page will show up to let you choose the track type. Let’s first choose “Annotation/RefSeq(genefile)” (red circle 2).

Another page will show up. In this page, first specify a name for the track (red circle 3), and then choose a annotation file by clicking “Browse...” (red circle 4). The gene structure annotation can be found from where your genome database is installed. For example, if your database is located at D:\genomes\mouse\mm8\, then you should choose D:\genomes\mouse\mm8\genefile\mm8.genefile.

After you click the “Update Track” button, your session page will be updated, and a new track that shows gene structures will be added.

 

You can follow similar steps to add DNA sequences and conservation scores manually.

For example, to add sequences, you can choose track type = sequence, and using folder D:\genomes\mouse\mm8\.

To add conservation scores, set track type = conservation, and folder = D:\genomes\mouse\mm8\conservation\phastcons\

At this point, you’ve already learnt a lot about CisGenome Browser. However, until now it was mainly used to visualize genomic regions. Indeed, the CisGenome Browser can also be used to visualize raw tiling array images and motif sequence logos. The visualization of raw array images has already been explained in session 2: tiling array analysis, and we will explain how to visualize motif sequence logo’s in session 5: motif analysis.

Since you’ve already learnt one of the most important functions of CisGenome, it’s time for you to take a break, reward yourself with some drinks and cookies. After the break, we will move on to the exciting sequence and motif analysis!  Next >>