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ProtoNet: Site Map.

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Type: Analyzing ProtoNet

Query: Get clusters having proteins with keywords

This utility is accessible from the "navigation tools" page and allows the user to get a list of all clusters where a given keyword appears.

Step 1:

    You have two options:
  1. Enter an exact keyword name
  2. Check the option box and enter part of a keyword
Protolevel

Step 2:
Given the results of your keyword-based search, click on a keyword to receive the list of clusters containing proteins matching the specific keyword.

 

Step 2: Query: Get clusters having proteins with keywords

5 keywords found in Arithmetic 40.28
containing "serpin"

Click on a result to continue:

| SwissProt (1) | | SCOP (3) | | GO (1) |

No. Type Keyword Number of proteins in DB with this keyword PANDORA *
/www/
 
SWISSPROT (1 keywords)   / up /
1SWISSPROT serpin 163 >>
 
SCOP (3 keywords)   / up /
1SCOP: fold serpins 9 >>
2SCOP: superfamily serpins 9 >>
3SCOP: family serpins 9 >>
 
GO (1 keywords)   / up /
1GO: Molecular function serpin 165 >>
* - this feature is currently only available in Advanced mode, for clustering "Arithmetic 40.28"

 

Step 3:
From the list of corresponding clusters, click on a cluster to see its cluster card.

 

Query: Get clusters having proteins with keywords

38 clusters with keyword:
serpin
Type - GO: Molecular function

The total number of proteins with this keyword is: 165 [ Get list of proteins ]
View PANDORA * (Protein ANnotation Diagram ORiented Analysis)

Sorted by: "Specificity-Purity score" [ default ] (descending )

NumIN - number of proteins in cluster with this keyword
NumOUT - number of proteins with this keyword out of cluster
No. Cluster ID Cluster size NumIN Specificity-Purity score Keyword
Deviation from Expectation
NumOUT
  sort by Cluster ID (descending) sort by Cluster ID (ascending) sort by Cluster size (descending) sort by Cluster size (ascending) sort by NumIN (descending) sort by NumIN (ascending) sort by Specificity-Purity score (ascending) sort by Keyword Deviation from Expectation (descending) sort by Keyword Deviation from Expectation (ascending) sort by NumOUT (descending) sort by NumOUT (ascending)
12254231601590.963330.446
22220061581580.957330.437
32177751571570.951329.388
42149881521520.921324.0913
52126291451450.878316.5320
62098631441440.872315.4321
72095481321320.8301.9933
82083421181180.715285.5147
920713160600.363203.53105
* - this feature is currently only available in Advanced mode, for clustering "Arithmetic 40.28"

 


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