Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression.
Stefanie De Bodt, Sebastian Proost, Klaas Vandepoele, Pierre Rouzé, Yves Van de Peer
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- CORNET web tool for integration of our predicted data with public PPI and co-expression networks
1. Query Arabidopsis protein-protein interactions
OPTION 1: Paste one or more proteins (AGI code) to retrieve the interactions they take part in:
Show only pairwise interactions between selected proteins
Also show the interactions between the neighbours of the selected proteins
OPTION 2: Search via TAIR gene description:
Show only pairwise interactions between found proteins
Also show the interactions between the neighbours of the found proteins
2. Download Supplementary data
Download supplementary figures and table
Figure S1. Calculation of GO similarity score. All possible GO terms of two proteins are compared in a pairwise manner. For each pair of GO terms (in green), the depth of the common ancestor (in blue) of these terms is calculated. The maximum depth of all pairwise combinations of GO terms is considered as the GO similarity score between two proteins.
Figure S2. Assessment of combinations of genomic features.
Figure S3. Overlap of the filtered (1) and predicted (2) interactome with previously experimentally shown (A) and predicted protein-protein interactions (B).
Table S1. False positive rates for different combinations of genomic features (BP=biological process, CC=cellular component, PCC=Pearson Correlation Coefficient)
Download table on GO evidence (Table S2)
Download table on contradictory CC annotation (Table S3)
Download filtered protein-protein interactions in text format (Table S4)
Protein-protein interactions that passed the genomic feature filters. BP score >= 8, CC score >= 5 or BP score>=5 + PCC >=0.3)
Download predicted protein-protein interactions in text format (Table S5)
Extension of filtered interactome. Interactions with orthologous group combination already present in filtered interactome are included
Download CAST clusters of predicted interactome and overrepresented GO categories (Table S6)
3. View Arabidopsis protein-protein interactions discussed in our manuscript (opens Cytoscape)
TRANSMEMBRANE ACTIVITY
ORGANELLE
CYTOSKELETON
RESPONSE TO
CELL CYCLE + DNA REPAIR + DNA REPLICATION
ATP_BINDING
LIPID
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