Input files

• Standard format of the biological network data file
• Standard format of the molecular profiling data file
• Standard format of the patient survival data file
• Download sample data files

• Standard format of the biological network data file [top]

  The network data file contains all the edges of a biological network, in which each line has two tab‑separated molecular IDs (protein or gene name) representing two endpoints of an edge. Here is an example of network data and the corresponding network graph.

  NOTCH1     NFKB1 NFKB1        AR CTNNB1     AR CTNNB1     NFKB1 TP53BP1     NFKB1

• Standard format of the molecular profiling data file [top]

  The molecular profiling data (e.g., microarray gene expression data or methylation data) is a tab‑separated numeric matrix, where the column names are the sample IDs and row names are gene IDs. The gene IDs should be consistent with network data, i.e. the same molecules must have identical IDs in both data files. The sample IDs should be the same as the ones in the survival data file. Specifically, the first line of the file has N tab‑separated sample IDs. From the second line to the end, the first column contains gene IDs and the other columns are numeric. For example,

  S1     S2     S3     S4
  NOTCH1     0.4     0.2     1.5     1.5
  CTNNB1     0.6     0.9     0.5     1.5
  TP53BP1     0.5     1.2     2.2     1.5
  
• Standard format of the patient survival data file [top]

  The survival data has three columns, named "id", "censor", and "time", respectively. The "id" column contains all the sample IDs, which should be the same as what are used in expression data. For the samples who died (censor=1), the corresponding numeric values in the "time" column represent the actual survival time. For the samples who were still alive until the end of the research or were failed to finish the study (censor=0), the time variables are the partial or incomplete survival time. Note: The first line of the data file contains three tab‑separated column names, which should be exactly "id", "censor" and "time".

  id     censor     time
  S1     0     3.133
  S2     1     58.1667
  S3     0     60.000
  S4     1     17.467
  
• Download sample data files [top]
  • Biological network file
  • Molecular profiling file
  • Patient survival file