Question: expression to networking
0
gravatar for krushnach80
2.3 years ago by
krushnach80630
krushnach80630 wrote:

I would like to know how to proceed from my gene expression data to building a network from that expression data .

So far what im doing is checking the differential expression of genes and see how it changes ..but that wont give me a global picture i suppose ..So it would be helpful if anyone can suggest me how do i proceed what kind of approach should i take .Suggestion would be really appreciable

rna-seq • 905 views
ADD COMMENTlink modified 2.1 years ago by xanderpico170 • written 2.3 years ago by krushnach80630

First: Get the list of genes that are most significant deferentially expressed using a statistical package like DESEQ2

Second: Pass the gene list to StringDB

Third: Import the output of StringDB to Cytoscape

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by YaGalbi1.4k

so i wont be doing any ranking of deferentially expressed genes which i have from Deseq2 , i could just put the huge list to string DB? lets say i have 1000 diff expressed genes , would it be meaningful to pass the gene list to string DB?

ADD REPLYlink written 2.1 years ago by krushnach80630
1

Well the basic principle of plotting a network of related genes is that you must try to plot a network of RELATED genes. So rather than passing a RANDOM gene set we first make a set of genes with something in COMMON (e.g. a differentially expressed gene set, or co-expression gene set, or tissue specific gene set etc. ) in the hope that a biologically meaningful network can be constructed.

The key word here...is HOPE.

I would rank the significantly differentially expressed genes by padj and select then the top 1000. Hopefully you will get some nice networks in there. But expect to see lots of unconnected genes.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by YaGalbi1.4k
3
gravatar for aka001
2.3 years ago by
aka001190
Sweden
aka001190 wrote:

That would depend on your experimental design and what kind of biological questions you have in mind, I would say.

You can check BioLayout 3D package (http://www.biolayout.org/) and check their tutorials. You can build some network together with the visualization through that package and I also found their tutorials really helpful.

ADD COMMENTlink written 2.3 years ago by aka001190
1

Biolayout 3D has been deprecated and is no longer supported..Miru (https://kajeka.com/) is its successor and is faster and more optimised than its predecessor..

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by prasundutta87360
3
gravatar for Corentin
2.3 years ago by
Corentin430
Corentin430 wrote:

If you have access to the enzyme annotations for your genes, you can use the KEGG API which can link enzymes to kegg pathways (http://www.kegg.jp/kegg/rest/keggapi.html). You can use R (or your favorite language) to access the API.

The file to link enzymes and pathways is available here : http://rest.kegg.jp/link/pathway/enzyme.

The advantage of this approach is that you can color your enzymes according to up-down regulation.

ADD COMMENTlink written 2.3 years ago by Corentin430
3
gravatar for xanderpico
2.1 years ago by
xanderpico170
xanderpico170 wrote:

Perhaps a bit late, but given a single differential expression result, I typically go to a resource like GeneMANIA to generate a network based on more comprehensive co-expression analysis and then import that into Cytoscape. Then I overlay my diff exp data onto that network to assess the "functional" modules being regulated in my dataset.

ADD COMMENTlink written 2.1 years ago by xanderpico170
1
gravatar for mforde84
2.3 years ago by
mforde841.2k
mforde841.2k wrote:

WGCNA comes to mind. Though coexpression networks need a lot of samples to be accurate.

ADD COMMENTlink written 2.3 years ago by mforde841.2k

well yes....but apart from that ?anything i have this flowchart can you give me more insight flowchart

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by krushnach80630
1

There's like 40+ pages of documentation on WGCNA... You can do it! I have faith in you!

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by mforde841.2k
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