Hello,

I am a newbie in the omics field. Currently, I am working on a proteomics dataset, which consists of gene list and expression values at 5 different time points, without replicates. I would like to perform network analysis on this data. I have applied following ways to analyse my data.

1. Clustering based on gene expression patterns -> Enrichment using "David" tools -> network creation using "Revigo" -> visualize using Cytoscape

Here, I was not able to change the node or edge properties. I am not use what's causing this problem, may be the issue is with revigo output. If anyone can help me out with this, that will be great.

1. Clustering -> String/Gene mania analysis -> network visualization

Although, I can do this, I wanted to do some unbiased approach, by considering the entire dataset, for a data set with only 2 conditions, (ex. normal vs tumor), the comparison is easier and with replicates in place, I will also be able to do differential expression analysis. However, I was thinking it's not possible with dataset I am dealing with.

If I have to consider fold change, I need to calculate taking every time point, which leaves me with 4 different fold changes (when I take first time point as control and compare other time points with it). I would like to know if there are any other ways to get around this problem or how to create a network based on these four different fold changes.

I am also looking forward to use other plugins available and drill more data from this. I want to follow an unbiased approach and visualize the "entire dataset" I have. Is this possible with the kind of data I am using here?

Are there any other ways of analyzing this kind of data?

I went through previous questions similar to issues I have here, but couldn't really get a solution. I am looking forward to suggestions from this great community.

Thank you