TUTORIAL
Protein-protein interaction network
The protein-protein interaction (PPI) network, MePPI-In, of cassava was constructed by using cassava genome version 4.1 (Phytozome version 9.0) based on interolog method. The PPI information from seven template plants (Arabidopsis thaliana (Arabidopsis), Solanum tuberosum (potato), Zea mays (maize), Oryza sativa (rice), Ricinus communis (castor bean), Populus trichocarpa (poplar) and Glycine max (soybean) were collected from seven databases; IntAct, MINT, AtPID, AtPIN, PAIR, APID and PRIN. In addition, co-expression and domain-domain interaction (DDI) information were employed to increase the reliability of the network. The confidence scores (CV; Thanasomboon et al, 2017) represent the reliability of the predicted interaction on basis of the quality and quantity of the employed data for prediction. For interolog-based method, the confidence of the prediction was given according to the types of method for identifying the PPI in the template organism, and the number of the data leading to a PPI prediction. For DDI-based method, the potential of the predicted PPI relies on the statistical significance of the finding DDIs between a protein pair wit respect to random opportunity (see more details in Thanasomboon et al, 2017).
1 |
Search cassava protein by using Phytozome ID or Uniprot ID |
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2 |
Search any words in the result table |
Description of terminology
| Protein ID | : A protein interacting with the searched protein in the formatted name as shown in Phytozome database (cassava genome version 4.1) |
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| Other name | : An alternative protein ID name in Uniprot database |
| Supporting evidence | : Two types of information supporting each PPI (gene/protein co-expression or domain-domain interaction (DDI)) |
| Source | : Database(s) providing PPI of template plant |
| Template plant | : Number of template plants involving in an inference of cassava PPI |
| No. DDI | : Number of domain-domain interactions supporting each inference of cassava PPI |
| CV grade | : Classification of predicted PPIs based on confidence level; Basal (B) : only interolog approach inferring High (H) : interolog approach inferring with DDI support H1 (CV score ≥ 80th percentile) H2 (50th ≤ CV score < 80th percentile) H3 (CV score < 50th percentile) |
| CV score | : Confidence value of each predicted PPI in the range of 0 to 1 |
| CV percentile | : The percentile of CV score of a predicted interaction CV = 0 (only interolog approach inferring) 0.14 ≤ CV score ≤ 1 (H1: Highest confidence) 0.12 ≤ CV score < 0.14 (H2: very high confidence) 0.01 ≤ CV score < 0.12 (H3: High confidence) |
| CV percentile | : The percentile of CV score of predicted interaction |