WIPER is the abbreviation of Weighted In-Path Edge Ranking, which can help evaluate all the biomolecular interactions/associations ("edges") in a network model to generate a rank order of them, based on their in-path traversal scores and a statistical significance test result.
WIPER can help biology users to highlight potentially critical molecular signaling or gene regulatory events in the network model. To validate whether WIPER worked as designed, we first tested the algorithm on a synthetic network model. Our test results showed that WIPER can reliably discover both critical “well traversed in-path edges” which are statistically more traversed than normal edges and “peripheral in-path edges” which are less traversed than normal edges. Compared with other simple measures such as betweenness centrality, WIPER provides better biological interpretations.
WIPER can take the input of weighted edges and rank them in a probabilistic network. In contrast, a conventional “edge betweenness” measurement that simply counts the number of shortest paths for any given edge would not be useful in practice. This makes WIPER a more pragmatic tool to solve biomedical problems such as finding a therapeutic strategy by "targeting the right interactions in the interactome". WIPER can provide a list of ranked-order edges and attributes together as follows:
| Attributes | Description |
|---|---|
| Edge | The edge identifier using the colon to separate the two endpoints, e.g. a:b. |
| Degree | The edge degree calculated in the "edge-to-edge" network |
| W[0] | WIPER's initial edge score calculated by the method same to rp score calculation described. |
| UFC | Usage Fold Change score calculate using the WIPER score divided by the medium of the WIPER scores' distribution. |
| logUFC[0] | log2-based Usage Fold Change score |
| UFC[0] rank | The WIPER edge ranking based on UFC[0] score |
| UFC[0] rank in network | The WIPER edge ranking based on UFC[0] score in each isolated networks, e.g. 1(a:b) means the edge is ranked the 1st in the network containing the edge a:b. |
| p-value[0] | The UFC[0] score's p-value from the distribution of UFC[0] scores. |
| significance[0] | The UFC[0] score's significance from the distribution of UFC scores. - represents p-value>0.05, * represents p-value≤0.05 and p-value≤0.01, ** represents p-value≤0.01 |
| W[2] | WIPER's iterative edge score calculated by the method described (WIPER: Weighted in-path edge ranking for biomolecular association networks, under submission.). |
| extended | 'No' indicates seed edges, 'Yes' indicates novel edges. |
| Parameters | Description |
|---|---|
| Interaction | A list of the edges consists of "nodeA", "nodeB", and "edge confidant score". The elements and edges are seperated by space. |
| Sigma | A damping factor varied from [0,1] determines the probability of a node continue in an information flow. |
| ppi | The threshold of edge confidant score. |
| method | "ant" represents the ant colony algorithm described in the paper "WIPER: Weighted in-path edge ranking for biomolecular association networks". 'page' represents a page-rank algorithm |
| interaction | The default iteration is 200 in the paper method. |