Protein protein interaction network

Question

[Tomk]

Hi, all I am new in protein interaction and also analyzing RNA sequencing data.

I draw this plot by this code below using R.

Read my PPI data

ppi_data <- read.csv("D:/ppi.csv", header = TRUE)

Create a graph from the data

ppi_network <- graph_from_data_frame(ppi_data, directed = FALSE)

Plot the network

plot(ppi_network, ertex.label.cex = 0.5, vertex.size = 5)

Structure of the data

str(ppi_data)

'data.frame': 24334 obs. of 3 variables:

$ node1_name: chr "Klf6" "Klf6" "Klf6" "Klf6" ... $ node2_name: chr "Ccnd1" "Kdm6b" "Kat2a" "Hdac1" ... $ score : int 722 430 622 691 765 927 433 420 543 430 ...

In this case I only observed interaction between each protein. Is there anyway that I can get also interaction among the proteins and interaction with central protein? (other common tools..?)

Thanks sincerely,

TH

[dthorbur]

You cannot get direct evidence of protein protein interactions from RNAseq data alone. You can only infer co-expression from this data, which can point towards an interaction, but is only a correlation. You can then verify candidate interactions through a method like co-immunoprecipitation (coIP). Additionally, you have not provided any information about the sample preparation and experimental design which will also affect the inferences you can make.