8. Examples » 8.1 Quick Walk-through

8.1 Quick Walk-through

Last modified by Lisa on 2012/11/21 14:38

The Regulome Explorer: All Pairs application allows the exploration of significant pairwise associations discovered within a heterogeneous dataset containing clinical, sample, and molecular data for hundreds of patients.  These datasets typically represent a single tumor type, but pan-cancer analyses are also possible.  The clinical information includes features such as age, tumor-stage, and histology, while the sample information includes features derived from molecular data such as single- and multi-platform cluster assignments and somatic mutation rates.  The molecular data may include any or all of the following types of high-throughput data:  mRNA and microRNA expression levels, protein levels, copy-number alterations, DNA methylation, and somatic mutations.

Regulome Explorer: All Pairs can be used in many ways.  Two use cases are:

1.  Examine associations for a specific gene.

2.  Examine associations for combinations of data types such as Gene Expression and Somatic Copy Number. 

You can try the following examples at

explorer.cancerregulome.org/all_pairs/?dataset=brca_manuscript_rerun_nov12d_pw

1.  Gene Search for Associations for a specific gene - BRCA1 

Below is an example of using RE:  All Pairs to look at associations with BRCA1.

In the filter window:

Click on reset if you have already used the Filter.

Enter these filter parameters:

Under Feature 1,

Type - All

Label - BRCA1

Click on Filter  

The filter will look like this:

Regulome Explorer All Pairs - Quick Guide Filter.png

The Genome-level View will look like this:

Regulome Explorer All Pairs - Quick Guide BRCA1 Associations.png

2.  Examine associations for combinations of data types such as Gene Expression and Somatic Copy Number.

In the filter window:

Click on reset if you have already used the filter. 

Enter these filter parameters:

Under Feature 1, 

Type - Gene Expression

Under Feature 2,

Type - Somatic Copy Number

Under Association,

Select >= for Correlation

Click on Filter 

The filter will look like this:

Regulome Explorer All Pairs - Quick Guide GEXP CNVR Filter.png

The Genome-level View will look like this:

Regulome Explorer All Pairs - Quick Guide GEXP CNVR Associations.png

You can hover over a tile to see the Information Card for a feature.  You can hover over an association to see the Edge Card for an association. 

Regulome Explorer All Pairs - Quick Guide GEXP CNVR Information and Edge Cards 2.png

You can click on an Association to see the Details Window which shows the data underlying the association:

Regulome Explorer All Pairs - Quick Guide GEXP CNVR Details 2.png

You can look at the Chromosome-Level View by clicking on a gene.  In this example, clicking on PARP1 will generate this view:

Regulome Explorer All Pairs - Quick Guide PARP1 Chromosome View.png

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Created by Lisa on 2012/08/16 10:29

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