Question: Identification Of Genes (Computationally) Driving Pathways
3
gravatar for Dataminer
6.8 years ago by
Dataminer2.7k
Netherlands
Dataminer2.7k wrote:

Hi!

I have a RNA-seq data from three different samples and when I compare the expression of genes in a certain pathway (for example say Cell cycle) I see that majority of genes in sample1 are upregulated compared to expression of genes in sample 2 and 3. The expression of majority of genes in sample 3 is repressed (comparatively), while sample 2 shows mixed trends compared to sample 1 and 2.

I am interested in identifying the genes that are master regulators of a pathway that will enable me to draw conclusion or atleast give indication if these pathways are down or upregulated.

Is their a way to find master regulators of pathways or a list of master regulators is available some where or has it been already published which can be used?

Any suggestions?

Thank you

pathway rna-seq • 2.6k views
ADD COMMENTlink modified 6.8 years ago by brentp23k • written 6.8 years ago by Dataminer2.7k
1
gravatar for munch
6.8 years ago by
munch300
Munich
munch300 wrote:

Maybe CluePedia can help you here. Here is an example: http://www.ici.upmc.fr/cluepedia/CluePedia_Fig1_Example.pdf

From the website:

CluePedia provides a holistic view on a pathway or process by investigating experimental and in silico data from different perspectives: gene interrelations revealed by correlation weights, miRNAs regulatory aspects, protein - protein interactions as well as the functional context, in conjunction with ClueGO. This review is helpful for defining new hypothesis and strategies that allow one more step in understanding complex processes. The CluePedia ClueGO/Cytoscape plug-in is user friendly and has an expressive and intuitive visualization.

ADD COMMENTlink modified 6.8 years ago • written 6.8 years ago by munch300
1
gravatar for brentp
6.8 years ago by
brentp23k
Salt Lake City, UT
brentp23k wrote:

You could look into "key driver analysis" or KDA for microarrays. This paper has a nice description and use: http://www.biomedcentral.com/1752-0509/5/121

from the paper:

One primary goal of gene network analysis is to identify key regulatory components, or key drivers, of sub-networks with respect to varying biological contexts [25,27]. The KDA takes as input a set of genes (G) and a gene causal (directed) network N. The objective is to identify the key regulators for the gene sets with respect to the given network.

There are modules to do KDA in cytoscape.

ADD COMMENTlink written 6.8 years ago by brentp23k
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