Tutorial: Protein Search

 

Tutorial Home

1.1. Quick-run examples

1.2. Simple search

1.3. Advanced search

1.4. Top genes and pathways

 

1.1. Quick-run examples

ActiveDriverDB was created to visualise and explore mutations affecting PTM sites in human proteins. The “Example” section of the homepage provides an illustration of the main visualisation plots created by ActiveDriverDB:

  

To get a quick first impression for ActiveDriverDB and explore these plots, you can click any of the four examples under the “Example” heading on the homepage:

Clicking the protein name will take you to the Sequence View tab of the search results. Alternatively, you can click on the “Network” button to navigate directly to the Network View tab of the search results. Both the Sequence View and Network View plots are fully interactive, allowing you to zoom in/out, move the objects around, and navigate to supplementary pages. Additional information regarding the various features can be viewed by clicking the [?] icons found throughout the pages.

 

1.2. Simple search

ActiveDriverDB allows you to search for any protein or mutation of interest by using the main search bar located on the homepage: 

 

 

Alternatively, you can use the smaller search bar located at the top right of every other page.

 

 

To navigate to the home page, you can type in https://activedriverdb.org/ into your browser, or click “home” or the “ActiveDriverDB” logo at the top left of the page you are on.

When searching for your protein of interest, you can look for either the protein name or the protein ID. Furthermore, you can also search for the specific protein or DNA mutation of interest by indicating the specific amino acid or basepair where the mutation was reported, respectively.

 

Type 

Example

Protein ID

TP53, NM_000345

Specific Protein Mutation

(Amino Acid Change) 

 TP53 R282W

Specific DNA Mutation

(Basepair Change; hg19/GRCh37) 

 chr12 57490358 C A

  

1.3. Advanced search

As an alternative to the simple protein/mutation search, you can also search for your queries using the advanced search page accessible under the homepage search bar:

 

Advanced protein/mutation search provides you with several advantages over simple search:

• Toggle between showing all mutations and mutations affecting PTM sites only

• View additional information regarding search query (e.g. genomic location, number of PTM sites, number of mutations, protein length)

• Search for multiple queries at once (one per line)

• Upload VCF files

• Search for partial search terms (e.g. “TP” rather than “TP53”)

 

1.4. Top genes and pathways

In addition to searching for your protein or mutation of interest, you can browse through our ranked lists of top-most mutated proteins/genes and pathways in inherited diseases and cancers as identified by genomic sequencing:

 

 

By selecting the appropriate ranked list, you will be taken to a different page containing the requested ranked summary table with genes or pathways (more information below).