How do I make subgroups?

Use the find samples feature (highlighted below) to make subgroups:

First, search for all the patient's samples you want in one of your subgroups. Next, click the Filter + Subgroup menu and choose 'New subgroup column'.

This will create a new subgroup column. All the patient's samples that matched your search term will be in one subgroup labeled as 'true' and all the samples that did not match your search term will in the other subgroup labeled as 'false'.

Your new column can be used for a KM analysis or to compare gene expression.

More information:

• How to search for samples

• Search terms for filtering and subgrouping

Example

In this example we are creating two subgroups in the TCGA Lung Adenocarcinoma study: patient's samples with aberrations in EGFR and those without. These aberrations could be mutations or copy number amplifications.

Steps

1. Type '(mis OR infra) OR C:>0.5' into the samples search bar. This will select samples that either have a missense or inframe deletion '(mis OR infra)', or where copy number variation (column C) is greater than 0.5. Note that I arbitrarily choose a cutoff of 0.5.

2. Click the filter menu and select 'New column subgroup'. This will create a new column that has samples that met our search term marked as 'true' (ie. those that have an EGFR aberration) and those that did not meet our search term as 'false' (ie. those that do not have an EGFR aberration).

For more information see our Basic Tutorial: Section 2.

See our help on renaming the subgroup labels from 'true' and 'false' to something more biologically meaningful.