6. Setting Filter Conditions

6. Setting Filter Conditions

Last modified by Lisa on 2012/12/11 08:28

You can use the Filter panel to look at data of interest.  You create a filter and then press Filter to run the filter.  The Genome-level view will then reflect the filter results.  Reset resets the filter but does not reset the genome-level view.  To return to a default view, click on Reset and then click on Filter.

There are several filter fields under 4 sub-headings :

  • Feature 1
  • Feature 2
  • Association
  • Distance

Feature 1 and Feature 2 correspond to the endpoints of an association arc.  Under Feature 1 and Feature 2, the following fields are present:

  • Type allows filtering by a specific type of experimental feature (for example, gene expression) or by pathway.  The default is All.
  • Label allows filtering by gene symbol (ex. SCN5A).  This field allows inclusion of an asterisk for wildcard matching (ex. APC*)
  • Chromosome allows filtering by chromosome number.
  • Position - Start and Stop allow filtering by genomic coordinates. 

Association corresponds to the arc joining two endpoints.  Under Association, the following fields are present:

  • -log10(p) <= can be used to specify an upper limit on the negative base-10 logarithm of p-values to display results up to a particular significance value.
  • Correlation can be used to filter by Spearman’s correlation coefficient value.  You can select a numeric operation and a specific numeric score.  There are 4 numeric options in the pull-down window:
    • >= greater than or equal to a specific value
    • <= less than or equal to a specific value  
    • Abs is Absolute value.  For example, Abs=0.5 means displays aggressiveness scores >= 0.5 and <=-0.5.   The default value is Abs=0.
    • Btw is Between.  For example, Btw=0.5 means display aggressiveness scores between -0.5 and 0.5.
  • # of samples >= can be used to display only those associations that have more than the specified number of underlying data points.
  • Order by can be used to order results based on one of the filter fields.
  • Max results specifies the maximum number of results to display in the genome-level view.  Please note that the time required to load the display is dependent on the maximum number of results that need to be loaded. 

Distance corresponds to the genomic distance between features.

  • Inter-Chromosomal
    Cis - indicates that the association should be within a chromosome.  Clicking on Cis activates the Distance option.
    Trans - indicates that the association is between different chromosomes
  • Distance
    >= greater than or equal to a specific distance
    <= less than or equal to a specific distance
    Distance - a numeric value for distance in kbp

The Filter by option allows filtering by Feature 1, Feature 2 or Association.  The default is Filter by Association.  

Here are a few examples of filtering associations:

1.  Gene Expression Gene Search

Click on reset if you have already used the filter.

The filter should look like this:

Regulome Explorer All Pairs - brca1_filter.png

Now, click on Filter to see the results.

2. Chromosome Search

Click on reset if you have already used the filter.

The filter should look like this:

Regulome Explorer All Pairs - chromosome_filter.png

Now, click on Filter to see the results.

3.  Associations between Somatic Copy Number and Gene Expression

In this case, add the Distance filter by clicking on the arrow next to Distance.  Set the filter to cis distance with <= 50 kbp to see the proximal associations.

Click on reset if you have already used the filter.

The filter should look like this:

Regulome Explorer All Pairs - cnvr_gexp_w_distance_filter2.png

Now, click on Filter to see the results.

Advanced Filtering Options

Using Isolate

If a specific feature label is entered under Label in Feature 1, you can observe the associations in a scatter plot rather than as association arcs.  Below is an example showing the use of Isolate with BRCA1:

Regulome Explorer All Pairs - Isolate.png

The scatter plot shows the -log10 p values for the associations between BRCA1 and other features.  Hovering over a feature displays an Information Card.

The scatter plot in the Isolate view can be modified by selecting Scatterplot under the Display Tab.  The Association, Plot Range, and Color Scale can be modified.  Select the option, enter the parameters, and then click Filter in the Filter Window to see the modified scatter plot.

Regulome Explorer All Pairs - isolate options.png

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Created by Lisa on 2012/08/16 10:07

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