Supported search terms for finding samples

Categorical features

Our search is 'contains' search, meaning the term you enter can be at the beginning, end or in the middle of a matched term. Our search is case-independent. An example is

IIA

will match 'Stage IIIA' and 'Stage IIA'. To specify a specific string, use quotes

"Stage IIA"

Numerical and Continuous features

You can specify a certain column and mathematical expression such as

A:>2

which will find all values greater than 2 in the first column. We support the following operators

= (equal)
>= (less than or equal)
>= (greater than or equal)
< (less than)
> (greater than)
!= (not equal)

Mutation data

You can search any annotation on a mutation, such as the functional impact, protein position, or gene name itself

To find all samples with mutations with the protein change, enter:

V600E

To find all samples where the functional impact has the text 'frame' or 'nonsense' in it:

frame OR nonsense

To find all samples that have a mutation, search the gene annotation:

TP53

To find all samples that do not have a mutation, use the negation of the gene annotation:

!=TP53

No data or 'null'

To find all samples that do not have data in one or more columns, use:

null

and choose 'Remove samples'. To find all samples that do not have data for just one column, use:

B:null

Sample IDs

Enter a sample ID to find a sample of interest. An example:

TCGA-DB-A4XH

If you are searching for multiple sample IDs, you will need to separate each by an 'OR'. You can copy and paste a list of sample IDs into the search bar as long as they are separated by a space, tab, or return (new line).

TCGA-DB-A4XH OR TCGA-2F-A9KO-01 OR TCGA-02-0001

Search a specific column

To make it easy to search a specific column, we use shorthand to annotate the first column as 'A:', the second as 'B:', etc. An example is

A:YES

This will search ONLY the first column for the word 'YES'. Note that we will retain your original search if you move the columns around.

Boolean operators: OR, AND, and !=

You can enter multiple search terms and we will match all of them with an implicit 'AND'. We also support 'OR'.

Use parentheses to group search terms. For example:

"Stage II" (B:Negative OR C:Negative)

will search for samples that match 'Stage II' in any column and are 'Negative' for either the second or third column.

You can also use '!=' to negate a term such as:

!=null

which will match all samples that have data across all columns.

Last updated 3 years ago

Was this helpful?