TRANSCRIPTINAL REGULATORY NETWORK MODULES

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2.5 years ago

SKY ▴ 60

I have a TRANSCRIPTIONAL REGULATORY NETWORK (TRN) made up of transcription factors (source) and genes (target). I want to divide the whole network in to parts (modules) depending on pathways and/processes the genes are involved in. How can i do it?

please help!

I am working with rice gene ids

tks Akash

REGULATORY MODULES RNA-SEQ TRANSCRIPTINAL NETWORK • 826 views

ADD COMMENT • link 2.5 years ago by SKY ▴ 60

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Do you have a mapping of the genes to pathways or you are trying to generate modules based on connectivity? It's not really clear. Also are you working with Cytoscape or other software? Cytoscape has a lot of plugins for various network analyses and it's easy to annotate your genes there.

ADD REPLY • link 2.5 years ago by Asaf 10k

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Thank you for your kind response. I am working with cystoscape. I want to group my network into modules based on pathways and NOT connectivity. I can get mapping of my genes to pathways. Can you please suggest tools?

ADD REPLY • link 2.5 years ago by SKY ▴ 60

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You can add it as nodes column data and then select specific pathways of interest generate new sub-networks.