transcriptome analysis

[ako...@gmail.com]

Hello, I want to ask a question about Cytoscape. I have a transcriptome data, I want to analyze the pathways, gene interactions and hit genes (with upstream and downstream targets) of my data. How can I use this application? I mean which tool is the most usefull for analysis that I aim? And I have a Macbook, can I download any tool, I am kind of new in this area. Thank you very much.

[piet molenaar]

Hi,

This is actually not a one-answer-question but a whole research project!

Basically it depends on what you're after; 

What is your research question?

What does my transcriptome data consist of?

Having defined that (and thought about it a lot ;-) there are basically two scenario's (or a combination thereof); either you find a list of differentially expressed genes from your data and try to find in what pathways they are found, or you map the transcriptome data on known pathways downloaded from public databases.

In both cases Cytoscape is useful; you'd probably want to start with a tutorial on basic expression analysis: http://manual.cytoscape.org/en/stable/Basic_Expression_Analysis_Tutorial.html

And some food for thought on visualization and the use of networks: https://www.slideshare.net/keiono/introduction-to-biological-network-analysis-and-visualization-with-cytoscape-part1

Hope this helps,

Piet

On Tue, Aug 8, 2017 at 12:44 PM, <ako...@gmail.com> wrote:

Hello, I want to ask a question about Cytoscape. I have a transcriptome data, I want to analyze the pathways, gene interactions and hit genes (with upstream and downstream targets) of my data. How can I use this application? I mean which tool is the most usefull for analysis that I aim?  And I have a Macbook, can I download any tool, I am kind of new in this area. Thank you very much.

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpdesk+unsubscribe@googlegroups.com.
To post to this group, send email to cytoscape-helpdesk@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/a4cd57a1-e2a9-4cb5-a47c-f75b7cb05b9e%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626