Size: 3133
Comment:
|
Size: 3622
Comment:
|
Deletions are marked like this. | Additions are marked like this. |
Line 17: | Line 17: |
SVM predictions were validated using known interactions from PDZBase, a domain peptide interaction database. The number of interactions which corresponded to known protein protein interactions (PPIs) from iRefIndex (BIND, BioGRID, CORUM, DIP, HPRD, !IntAct, MINT)was also calculated. | SVM predictions were validated using known interactions from PDZBase, a domain peptide interaction database. The number of interactions which corresponded to known protein protein interactions (PPIs) from iRefIndex (BIND, BioGRID, CORUM, DIP, HPRD, !IntAct, MINT) was also calculated. |
Line 19: | Line 19: |
The following are SVM proteome scanning predictions for human, fly and worm PDZ domains. The format of the output is: <predicted binder> <decision value> [PB|IR(.)] <transcript ids> |
The following are SVM proteome scanning predictions for 13 human, 6 fly and 6 worm PDZ domains with domain-peptide interactions in PDZBase. * [[attachment:HumanSVMPredictions.zip|Human 13 (zip)]] * [[attachment:FlySVMPredictions.zip|Fly 6 (zip)]] * [[attachment:WormSVMPredictions.zip|Worm 6 (zip)]] The following are SVM proteome scanning predictions for 192 human PDZ domains for which the SVM predicted binders. From this set 75 PDZ domains had predicted interactions which corresponded to PPIs in iRefIndex. Please see Supplemental Information for the identities of these domains. * [[attachment:Human192SVMPredictions.zip|Human 192 (zip)]] The format of the output is: <predicted binder sequence> <decision value> [PB|IR(.)] <transcript ids> |
Line 24: | Line 34: |
SVM Predictons: * [[attachment:HumanSVMPredictions.zip|Human (zip)]] * [[attachment:FlySVMPredictions.zip|Fly (zip)]] * [[attachment:WormSVMPredictions.zip|Worm (zip)]] |
|
Line 45: | Line 50: |
* iRefIndex interactions for Human) | * iRefIndex interactions for Human |
Line 47: | Line 52: |
* !ProteomeScan Files * Files required to run the !ProteomeScan software |
Proteome scanning of PDZ domain interactions using support vector machines
Contents
Background
An accurate predictor of genomic PDZ domain interactions would allow the proteomes of organisms to be scanned for potential binders. Such an application would require an accurate and precise predictor to avoid generating too many false positive hits given the large amount of possible interactors in a given proteome. Once validated these predictions will help to increase the coverage of current PDZ domain interaction networks and further our understanding of the roles that PDZ domains play in a variety of biological processes.
Results
We built an SVM using mouse and human experimental training data to predict PDZ domain interactions. We showed that it correctly predicts known interactions from proteomes of different organisms and compared to published state of art predictors, is more accurate and precise.
SVM Predictions
SVM predictions were validated using known interactions from PDZBase, a domain peptide interaction database. The number of interactions which corresponded to known protein protein interactions (PPIs) from iRefIndex (BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT) was also calculated.
The following are SVM proteome scanning predictions for 13 human, 6 fly and 6 worm PDZ domains with domain-peptide interactions in PDZBase.
The following are SVM proteome scanning predictions for 192 human PDZ domains for which the SVM predicted binders. From this set 75 PDZ domains had predicted interactions which corresponded to PPIs in iRefIndex. Please see Supplemental Information for the identities of these domains.
The format of the output is:
<predicted binder sequence> <decision value> [PB|IR(.)] <transcript ids>
- PB = Found in PDZBase
- IR = Corresponds to a PPI in iRefIndex (transcript index1, ..., transcript index n)
Supplementary
- Models
- Chen model parameter and binding site encoding files
- Stiffler model parameter files
- Proteomes
- Ensembl proteome files for Human, Worm and Fly
- Experiment Interaction files (in peptide file format)
- Fly files from Chen
- Human files from Sidhu
- Mouse files from Stiffler
- Worm files from Chen
- Curated Interaction files (flat files)
- PDZBase for Human (Worm and Fly included, but not used)
- iRefIndex interactions for Human
- Phage codon bias files
ProteomeScan Files
Files required to run the ProteomeScan software
- Models
Source Code
- jfreechart 1.0.12 (and dependencies)
- weka 3.9.1
auc calculator (Davis & Goadrich, 2006)
BioJava 1.5
- iText 2.1.3
- jmatio
- Bingo 2.3
- Cytoscape 2.6.3
- Cytoscape-task 2.6.3
- BRAIN 1.0.5 (pdzsvm)
- libSVM 2.8.9 (pdzsvm)
Team
- Shirley Hui
- Gary Bader