Advanced Search on TBDB
TBDB's Advanced Search provides the ability to search for gene annotations and gene expression data in TBDB and frame complex multi-step queries. These multi-step queries are displayed in a step-wise graphic interface with the option to edit any step. You can save your searches or share them with a collaborator.
Our example shows how to find:
- Genes that have solved structures,
- whose protein length is less than 300,
- which do not contain any epitope annotations, and
- whose gene expression in macrophages shows more than a two-fold change when comparing timepoints 4 h and 24 h after macrophage infection.
Here are the steps to achieve this:
From the menu under Protein Attributes
select Solved Structure.
On the following screen, click "Get Answer"...
...and you will get a list of results:
Continue by clicking on "Add Step", then select Protein Attributes > Protein Length.
Set the limit for proteins less than 300 aa long, then select INTERSECT as combination and click "Run Step":
Now we further limit the results by eliminating any genes with know epitope annotations.
Click "Add Step", then select Protein Features > Epitope Presence.
Check off all three epitope types, then select 2 MINUS 3 from the combination options and click "Run Step".
As the last step, select Transcript Expression > Microarray Evidence,
then choose M.tb human Macrophage infection (fold change) from the list of options.
In the following screen, select "24 h after macrophage infection" as the comparison time point, and INTERSECT as the combination mode:
The final result is a list of five genes:
Each step can be revised, renamed, incorporated into nested queries, weighted, or deleted at any time. Click on the step's name in the query diagram to initiate that process.
Further Options
You can take your list of gene results and download annotation data in the format of your choice, analyze expression data for those genes, or add them to your TBDB basket (you have to be signed in) to save them for future use.