Network analysis: where to start?

Question

[Mozart]

Hello there, I am really fascinated by the possibility to start developing a very simple tool for analysing networks, given a list of genes. firstly, I would like to stress that the aim is not to publish but just understand the basics needed to get into grip with this tool.

Before posting, I have read at this tutorial by Kevin and I would like to learn more about this. More precisely, I would like to understand how to study likely correlation between genes differentially expressed, if that makes any sense to you? In other words, where to actually start from?

[andres.firrincieli]

I would like to understand how to study likely correlation between genes differentially expressed, if that makes any sense to you?

just a thought but my understanding is that a correlation network built with differentially expressed gene is less informative than a simple heatmap with hierarchical clustering done for both the rows and the columns.

[Mozart]

I am more generally interested by determining how to mathematically calculate correlation between genes and how, from there, create a basic network structure.

[andres.firrincieli]

This is old but it is good start: link

Have fun!

Answer 1

[Bogdan]

if you'd like to take a look into :

https://github.com/gladstone-institutes/Bioinformatics-Workshops/tree/master/intro-pathway-analysis-visualization

https://github.com/gladstone-institutes/Bioinformatics-Workshops/tree/master/intro-pathway-modeling

and into more advanced workshops too.

[Mozart]

Thanks for that. Really helpful. Can you also provide hints on the above comments provided here, please?