Question: network analysis of differentially expressed genes
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gravatar for praveenhcu131
22 months ago by
praveenhcu1310 wrote:

how to do network analysis of deferentially expressed genes between two conditions please tell me the brief procedure and the tool to use

rna-seq R • 921 views
ADD COMMENTlink modified 22 months ago by theobroma221.1k • written 22 months ago by praveenhcu1310

What do you mean by network analysis ? What are the questions you want to address ? You can do plenty of analyses on networks (e.g. connectivity, paths, centrality, communities) but not all would be relevant to what you're interested in.

ADD REPLYlink written 22 months ago by Jean-Karim Heriche18k
1

the word network analysis is highly abused in the field. So be precise and clear of what is your intention of doing. Networks can be build on GO cateogies, disease pathways focusing on a particular one for your interest of research and build the network of the degs that gets enriched for pathways, or direct PPI interaction networks, or networks from motifs on DE target genes or gene regulatory networks built of master regulators. Does most of the term register to you? I guess all of it won't. I mean its endless. So please try to first understand what is the intent of study you want to do and which kind of biological question you want to address with a network analysis. Then you can focus on some papers and get to know the field and run tools and softwares. If then you face issues we can help.

ADD REPLYlink written 22 months ago by ivivek_ngs4.6k
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gravatar for EagleEye
22 months ago by
EagleEye6.2k
Sweden
EagleEye6.2k wrote:

I assume that you are asking about pathway enrichment analysis.

Use your gene list (per condition) in GeneSCF using KEGG as a reference database. It will give you results with enriched KEGG terms in each condition.

For presenation of the results please check this post.

ADD COMMENTlink modified 22 months ago • written 22 months ago by EagleEye6.2k
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gravatar for theobroma22
22 months ago by
theobroma221.1k
theobroma221.1k wrote:

I have to edit / update this post, but check it out It's about the journey, and not the destination

ADD COMMENTlink written 22 months ago by theobroma221.1k
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