Integration of data using reference genomic sequences. Users, Groups, Roles, Database, linking, sharing and up- and down-loading data. Tools; tabular views, track operators, editors. Using Galaxy for pipeline integration.

OUTLINE

1. Genboree User

User registration

2. Genboree Group

Creating a group

Adding users to a group

Setting user roles: Administrator, Author, Subscriber

3. Genboree Database

Creating a database

Template database

Custom database

Publishing a database

4. Genboree Tracks

Uploading tracks

File formats: LFF, Blat, Blast, Agilent Probes

Attribute-Value Pairs

Downloading tracks

Managing tracks

Annotation Editor

5. Links

Link into Genboree

Link from Genboree

To a Genboree internal view

To an external site

Send Link using "Email Group"

6. Tools

Search names by keyword

Tabular View

7. Galaxy Integration

EXERCISES

One of your collaborators has requested that you analyze their cancer deletion data. You will use Genboree and Galaxy in order to accomplish this.

1. In Genboree, create a database within the "Course 311-405: CAD 2009" group based on the Human (hg18) template. Use your name as the database name.

2. Download the BED file "cancerDeletions.bed" available on the lab information page. (http://genboree.org/java-bin/project.jsp?projectName=CAD_Course_2009/1-9-09)

3. Upload "cancerDeletions.bed" to Galaxy. The coordinates in this file are on hg17, so set the "Database/Build" to hg17 after uploading it.

4. Use the Galaxy "Lift-Over" tool to convert the cancer deletions from hg17 coordinates to hg18 coordinates. You may ignore the unmapped coordinates produced by the liftover.

5. Download into Galaxy the hg18 "UCSC Genes" track from the "UCSC Main table browser". Make sure to set the region to genome.

6. Use the Galaxy "Intersect the intervals of two queries" tool to find genes that intersect with cancer deletions. Make sure to use knownGene as the first query and the lifted over cancer deletions as the second query.

7. Use the "BED-to-LFF converter" to convert both the lifted over cancer deletions and the genes that intersect with cancer deletions into LFF format. For the lifted over cancer deletions use the following LFF values:

LFF Class: Cancer Deletion
LFF Type: Cancer
LFF Subtype: Deletion

For the genes that intersect with cancer deletion use the following LFF values:

LFF Class: Cancer Deletion
LFF Type: Cancer
LFF Subtype: Gene

8. In Galaxy, use the "Upload to Genboree" tool to upload the lifted over cancer deletions and genes to the Genboree database you set up in step 1.

9. In Genboree, link the "Cancer:Gene" track to UCSC hg18 browser using the LFF name.