Web Service for Yeast Protein-Protein Interaction Predictions (YPPIP)

 

 

    

 

 

Services:

 

 

Query Database

 

Getting Help

 

 

Downloads

 

 

Reference

 

Help:

Many fundamental biological processes involve protein-protein interactions. Comprehensively identifying these interactions is important to systematically defining protein cellular roles.

We studied three aspects related to combining multiple biological evidence to predict protein-protein interactions in yeast. The evidence includes not only the datasets that specifically look for protein interaction but also indirect information like mRNA expression data, protein-DNA binding data, protein localization data.

Here we provide a database retrieval service  to let users be able to search the full predicted scores for co-complex and physical interaction task.

(Note, we have to point out that the positive training data used here were collected in 2004. There are quite some bigger Yeast PPI data sets coming out recently. The predictions would be definitely improved with better and larger positive training set.)

 

1. Get Prediction Confidence Score

Input

User need to enter a pair of interested ORFs (or Gene Names) directly in the boxes provided. The user also needs to choose which predicted set to search. A minimum of two protein ORFs have to be chosen or entered to use this tool. One cannot find score for a protein interacting with itself. For instance, if ORFs 1 and 2 have been entered for the input parameters, the scores of the following pairs would be retrieved è pair  1_2

Example – 

Protein1

Protein2

Set

ORF or Gene Name

YAL001C

YAL002W

mipsSvm

ORF

 

Output

The output will be displayed as a text file in the following format
<Protein1> - Entered by user.
<Protein2> - Entered by user.
<Score> - Real value giving confidence score.

Example - 

Protein1

Protein2

Score

Set

ORF or Gene Name

YAL001C

YAL002W

-1.2673336

mipsSvm

ORF





2. Find Protein Interacting Partners

Input

One can find interacting proteins by entering an ORF or a gene name. A threshold can be set for the confidence score. Only pairs having confidence score greater than threshold would be retrieved.

Example – 

Protein1

Set

ORF or Gene Name

Score threshold

Search choice

YAL002W

dipsSvm

ORF

0

Find Partners In Threshold

 

Output

The output will be displayed as a text file in the following format
<Protein1> - Entered by user.
<Protein2> - Entered by user.
<Score> - Real value giving confidence score.

Example – 

Partner 1

Partner 2

Interaction Score

YAL002W (Gsf, Yeast)

YDL049C (Gsf, Yeast)

0.16581967

YAL002W (Gsf, Yeast)

YGR078C (Gsf, Yeast)

0.844582

YAL002W (Gsf, Yeast)

YJR075W (Gsf, Yeast)

0.5493458

 

 

 

3. Find Protein Interacting Partners Within a Group of Proteins

Input

One can find interacting proteins within a group of input proteins. Enter a group of ORFs or gene names. A threshold can be set for cutting off the confidence score. Only pairs within this group having confidence score greater than threshold would be retrieved.

Example – 

Proteins

Set

ORF or Gene Name

Score threshold

Search choice

YAL002W

YML094W

YLR148W

YLR396C

dipsSvm

ORF

0

Find Partners In Threshold Within List

 

Output

 A table of found pairs will be displayed as a text file in the following format. The edges would be displayed in SVG image format as well.

Example – 

Partner 1

Partner 2

Interaction Score

YAL002W (Gsf, Yeast)

YML094W (Gsf, Yeast)

0.5682917

YAL002W (Gsf, Yeast)

YLR148W (Gsf, Yeast)

1.250405

YAL002W (Gsf, Yeast)

YLR396C (Gsf, Yeast)

0.7392374

YLR148W (Gsf, Yeast)

YML094W (Gsf, Yeast)

0.8882086

YLR148W (Gsf, Yeast)

YLR396C (Gsf, Yeast)

2.0707695

 

 

 

 

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