Antibody microarray data; co-expression network

Question

[m3hdad]

I have a set of data from antibody microarray (kinexus).

There are 10 samples which consist of 5 different cell lines and for each there is a control and treated.

I was wondering if it is possible to use this set to construct a co-expression network and analyze.

I would appreciate if you could suggest other system biology methods for further analysis.

Answer 1

[Kevin Blighe]

It is not the greatest dataset for this purpose. In each cell-line, you have just a 1 versus 1 comparison. You cannot faithfully construct a co-expression network from just 1 or 2 samples.

An alternative would be to create separate networks for all controls (n=5) and all treated (n=5); however, even in that case, your sample numbers are low and it require mix the cell lines into a single group.

With such low numbers, you may simply consider deriving ratios of expression (treated / control) for each gene in each cell line.

Kevin

[m3hdad]

Thank you for your answer Kevin. I understand and we have already compared genes in each cell line. Now the idea is to investigate if there are other methods to further analyze the data.

[Kevin Blighe]

You should increase your number of replicates. Then, you could actually perform a proper differential expression comparison and hope to do network analysis.

Given the low numbers, and aside from simply deriving ratios of expression, you may consider some form of gene enrichment analysis using the genes that have the highest and lowest ratios (ratios derived from treatment / control).