GRN with RNA-seq data

[joness...@gmail.com]

Hello,

I am newbiee in GRN analysis. I read the istruction but not clear yet what I am doing.

I would like to use my differentially expressed RNA-seq data. would it be possible please to provide an input file for expression data?

 can I use your software  when my samples are not time course?

Thanks
Sara

 

[William Longabaugh]

Hello:

BioTapestry is not designed to infer a network from expression data, but
to visualize and organize a network that you have created.

So you are going to have to analyze your data using some other software
to take your differentially expressed RNA-seq data and use it to infer
network links. Once you have links, you can import your network into
BioTapestry either using a simple "SIF" file of links, or BioTapestry's
CSV file input format.

If you then want to import expression data that can then be viewed by
clicking on each gene, there is an example file provided with this
tutorial:

http://www.biotapestry.org/tutorials/dmt/DynamicModelsTutorial.html

A more complete definition of that input file format can be found here:

Longabaugh, W.J.R. BioTapestry: A Tool to Visualize the Dynamic
Properties of Gene Regulatory Networks. Methods Mol Biol. 786, 359-94,
2012.

Hope this helps.

Bill

> --
> You received this message because you are subscribed to the Google
> Groups "BioTapestry-users" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to biotapestry-us...@googlegroups.com
> <mailto:biotapestry-us...@googlegroups.com>.
> To post to this group, send email to biotapes...@googlegroups.com
> <mailto:biotapes...@googlegroups.com>.
> Visit this group at https://groups.google.com/group/biotapestry-users.
> For more options, visit https://groups.google.com/d/optout.