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"
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)
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
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
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
Use 'alt-click' to freeze for copying a sample ID from the tooltip.
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.
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.
How to find samples that you want to remove or keep in the view. How to make subgroups.
Use the search box at the top of the screen to first pick/find your samples of interest. Then filter to keep or removes these samples, create a new subgroup column, or zoom.
The bar highlighted above allows you to search all data on the screen for your search term. Note that it will not search data that is not on the screen. Samples that match your criteria are marked with a black bar in the Visual Spreadsheet.
You can search for samples by either typing in the search bar or by clicking on the dropper icon to enter the pick samples mode. The pick samples mode will allow you to click on a column to select samples. The search term for your picked samples will appear in the search bar. To exit the pick samples mode, click on the dropper icon again.
Note the pick samples mode tends to work best if the column you are selecting from is the first column.
More information on supported search terms
Once you have your sample(s) of interest, click on the filter + subgroup menu and choose to:
Keep samples: Keep only the samples which match your criteria.
Remove samples: Remove the samples which match your criteria.
Clear sample filter: Remove ALL filters currently applied.
Remove Samples with nulls: Removes samples that have no data for one or more columns. Equivalent to typing 'null' in the search bar and choosing 'Remove samples'.
Zoom: Zoom to the samples that meet your criteria. Shift-click to zoom out.
New subgroup column: Create a new column where samples that meet your criteria are annotated as 'true' and samples that don't meet your criteria are annotated as 'false'. This new columns can then be used for Kaplan Meier Analysis or in the Chart View.
To create more than 2 subgroups, please see our 'How do I make subgroups with geneA high and geneB high?' guide.
Once you have either filtered, created a subgroup column, or zoomed to samples, your search term will be added to the search history. Access the search history by clicking the downward facing arrow at the upper right of the search bar.
Note this search history will be preserved in bookmarks.
Once the subgroup column is created, users can change the labels from "true" or "false" to, for example, "wild type" or "EGFR mutant" by adjusting the column display settings. To access these select the three dot menu at the top of the column and choose 'Display'