Structure of a Protein-Protein Interaction Network

Question

[Saeed Rahmani]

I have a Protein-Protein Interaction data that get from this paper. In data we have two type: 1.Normal 2.Cancer

But in two type of data we have protein or connection that is equal. I think one of field will be weight that determine which of proteins has connection or Interaction.

The structure of data is:

which column is weight? or I right think?

[Jean-Karim Heriche]

If the data file has no column headers and the file structure is not explained in the paper, then you should contact the authors.

[Saeed Rahmani]

Authors no answer. In paper no things about data structure.

Answer 1

[Girolamo]

In my opinion, the decimal numbers in the table represent the expression of the proteins, according to what is written in the caption of the supplementary material: "Additional file 2: Expression and interaction data related to normal and cancer conditions of five tissues" Even if the numbers are quite strange because they are recursive somehow.

[Jean-Karim Heriche]

The data is in one file per tissue. The example provided by the OP comes from one such file. In the absence of clear indication, what each number represents is anybody's guess.

[Saeed Rahmani]

thank you. But each type has two decimal numbers, your mean is first decimal number column or second decimal numbers column?

[Jean-Karim Heriche]

In the absence of clear description, I would be wary about making educated guesses about what the data represent.

[Girolamo]

I think that the first decimal column refers to the first protein, and so on. For example: the expression for 4EBP1 is 157.88, the expression of AKT1 is 78.54 What is strange to me is that the 14-3-3, the CTNB1 and PIK3R1 have the same expression.

[Saeed Rahmani]

That's right. Thank you. They were use of DEU(Digital Expression Unit). After of weight expression make a digital expression unit and use of binary addition according showed in paper.