creating sub-network from a gene list in cytoscape

Question

[zizigolu]

HI,

I have a network in cytoscape and a list of about 40 genes which i want to extract sub-network of these genes from my network, how I can perform this please?

thank you

[zizigolu]

thank you Dear Jean-Karim Heriche

I selected my genes from select-nodes-from ID list file

[Shamim Sarhadi]

There is another option,you could map your gene-IDs on PPI network here http://http:www.networkanalyst.ca/faces/home.xhtml , then select a subnetwork based on a cut-off of degree,or you could simply perform module finder function,here is a nice tutorial http://www.networkanalyst.ca/faces/docs/FaqView.xhtml

[zizigolu]

merc Shamim ama chera bayad avval be protein-protein interaction tabdil konam?

[Shamim Sarhadi]

Mamulan ta jaei k man midunam, mishe network khode gene haro ham dakhele cytoscape visualize kard,ama bishtar in karo vase ppi anjam midan, yani genhaie k bayan shodan networkesho tu level PPI barrasi mikonan,va moshakhasate network mesle degree,BC,CC va ... tu level ppi tarif mishe ,az tarafe dg man fek mikonam vaghti genehaye bayan shode darim networko tuye level ppi analyze konim be vagheiat un phenotype morede nazar nazdiktare , omidvaram age eshtebah mikonam eslaham koni networkanalyst taghriban automat hast va hamechizo tozih dade

[zizigolu]

rastesh man ziad mosallat nistam be har hal kheili manun

[Shamim Sarhadi]

man networkanalysto chek kardam, gene name ke bedi khodesh ru ppi map mikone,age ye bar try koni motevajeh mishi chejurie movafagh bushi

[Ram]

I'd recommend you use English as other users will also be able to understand and contribute to the discussion.

[yuewu_mike]

So, is there any solution to select a list of nodes in cytoscape? I didn't quite find it in the answer, especially for a large node list. Sorry for the trouble

[Jean-Karim Heriche]

Besides the manual selection option described in my answer, there's also a possibility of filtering nodes and edges using the select panel. In particular, you can filter on a node attribute by using the column filter.

Answer 1

[ivivek_ngs]

You can check from the wiki link here, that should be handy to perform once you have the network set up. There is Network Analyzer setting which can help you to perform the task. Obviously you have answer here but in case you need a manual to see how to do look at the link.

Also @Jean-Karim Heriche made a similar reply few weeks back about selecting the components from network. Take a look at this thread.

I would request a bit , please do not think that I am being rude. But just that we already have answer for this question , creating same thread makes it redundant. So before posting if you can try and see threads in Biostars with tags like cytoscape and network to maximize the usage of the blog to one's benefit. It will be handy for any OP posting here and be more targeted in their query. Just a request.

[zizigolu]

I answered her? her and me are the same :)

you all right, thank you for your comments.

[ivivek_ngs]

It was a typo, I changed it. If you have your problem solved then the purpose is meted out.

[zizigolu]

thank again.

I was googling for this problem since yesterday and I could not find the solution but comments by @Jean-Karim Heriche in this post helped me to find the solution by searching in Cytoscape options then I shared the solution for possible OP who faces the same question.

[ivivek_ngs]

Nothing beats if OP answers their own question. The purpose of the blog caters to make one solve their problem not only from others answer/comments but also on their own and follow it up so that they can be confident in future to help others who are new to the forum. I am glad that you already posted your answer. Not everyone takes the onus to track back to reply to their own query if they solved.

Answer 2

[Jean-Karim Heriche]

In cytoscape 3.x there's a button in the menu bar at the top called 'New Network From Selection' (hover the mouse over it to see the name). As the name implies, it creates a network out of selected parts of a network.

[zizigolu]

sorry but I don't know how to select gene list from network, you thought me how to create network of selected genes. I have a list of genes I don't know how to select these genes firstly from network loaded in cytoscape.

thank you

[Jean-Karim Heriche]

Simply click on what you want to be in the subnetwork in the layout window. Hold shift or ctrl to select multiple nodes and edges or click and drag to select a region. This is probably easier as it will select both nodes and their edges whereas in the click approach, you need a click on each node and each edge you want to keep. If the network is large and you need to segregate you subnetwork in the layout to make selection easier, give the nodes a distinct attribute and use Layout>Group Attributes Layout.

[zizigolu]

sorry I have a list of genes I imported that by import-table then in Layout>Group Attributes Layout. option i selected this file but only few genes of my list is distinct from network which I can segregate them easily. my network is big I need to segregate these genes together from network. its my genes list shape I imported in cytoscape

Control-degree    control-betweeness    
COL5A2            DSG2
DSG2              TEK
COL5A1            COL5A2
COL15A1           PLAU
COL1A2            ITGAV
PCOLCE            EPB41L5
HTRA1             SASH1
ALDH18A1          ALDH18A1
PLLP              GRAMD2
AGER              CCDC85A