This is a web page for our ECv calculation software proposed by Tanaka et al. (2020). The software calculates an ECv for every input sample and edge given a Bayesian network model with B-spline nonparametric regression, that can be estimated by SiGN-BN. See our published paper for details of our edge contribution value (ECv) related information.
The software is freely available for academic, non-commercial users. Please concact Prof. Yoshinori Tamada, who is a developer of the software.
| ECv Calculator release | 0.8 (Wed Jan 25 16:24:04 2023) |
Please cite the following paper when you publish your results using ECv:
Tanaka, Y., Tamada, Y., Ikeguchi, M., Yamashita, F., Okuno, Y. (2020). System-based differential gene network analysis for characterizing a sample-specific subnetwork, Biomolecules 10(2), 306. https://doi.org/10.3390/biom10020306
For the indivisual network visualization using RC values, please cite the following paper:
Tanaka, Y., Higashihara, K., Nakazawa, M.A., Yamashita, F., Tamada, Y., Okuno, Y. (2021). Dynamic changes in gene-to-gene regulatory networks in response to SARS-CoV-2 infection, Scientific Reports 11, 11241. https://doi.org/10.1038/s41598-021-90556-1
For subtype identification of samples using an ECv matrix, please cite the following paper:
Nakazawa, M.A., Tamada, Y., Tanaka, Y., Ikeguchi, M., Higashihara, K., Okuno, Y. (2021). Novel cancer subtyping method based on patient-specific gene regulatory network, Scientific Reports 11, 23653. https://doi.org/10.1038/s41598-021-02394-w
NOTE:
- PATENT PENDING. DO NOT REDISTRIBUTE WITHOUT PERMISSION. THIS IS FOR ACADEMIC, NON-COMMERCIAL USE ONLY.
- THE FOLLOWING LINK IS VALID ONLY WHEN YOU ACCESS VIA A LINK SENT FROM THE DEVELOPER.
・ecv-0.8.tgz : Gzipped tar file (3,259,062 bytes)
Download the above file. Place it in your directory of HGC SHIROKANE via SCP. Or, use "curl -J -O above_clickable_URL" command at your directory of HGC SHIROKANE to download and save the package directly. Please make sure that your directory is not accessible from other users.
Expand the file by the tar command such as "tar xvfz ecv-0.7.tgz". The file "ecv" in the directory is the executable binary for HGC SHIROKANE. You can put the executable any directory where it is not accessible from other users.
Usage:Options:network The network file containing estimated network structure and its B-spline parameters. output The arbitrary output file name to store the calculated ECv. The file is a tab-separated text file. The first line is a header line showing the meaning of columns. Each row corresponds to an edge in the network file. If a node of an edge is not found in the network and/or the input data, then such edge is ignored for the calculation and not written in output. The first column of output represents a parent and the second its child. The following columns are ECvs for the samples in input. The order of columns are the same as input. input Input data file. The file needs to be a tab separated text file (EDF or GDF). Each row represents log2 transformed expression values of a node (variable, or gene). The first, left-most column represents the name of a gene followed by their expression values. Thus, a single column corresponds to a single sample. Node names should be the same as in the network file network. Otherwise, the software is not able to find the corresponding edges between two nodes in input. It is not necessary that input includes all the nodes in the network. If a node in input is not found in the network, then it is ingored. As noted above, if a node in the network is not found in input, then edges that include such nodes are ingored and not output in output.
- --method M
- Specifies the type of edge contribution values to calculate. M can be one of the following:
ECv : (This is default) Edge Contribution value.
RC : Relative Contribution value.
RC2 : Relative Contribution value, or -1 for single parent node.- --name
- Specifies to output the "parent_child" style unique "name" column so that users can match network edges and ECvs with Cytoscape.
- --mem N
- Specifies memory size N in MiB for ECv Calculation.
Suppose that all the required files are placed in the current directory. Execute the following command to calculate the ECv matrix as a file "output.txt".