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:

The Genome-level View will look like this:

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:

The Genome-level View will look like this:

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. 

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

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