Generating metabolic network

[Ankita Chatterjee]

I am new to network analysis using Cytoscape. I have names of metabolites and their associated reactions. How to generate a metabolic network in which nodes represent the metabolites and edges represent reactions (So, if two metabolites participate in the same reaction, they should be connected by an edge representing the reaction/enzyme)? 

Thank you.

[Scooter Morris]

HI Ankita,
   In principal, this is relatively easy.  All you need to do is to massage your list so that it looks like an edge list:

metabolite1 reaction1 metabolite2
metabolite1 reaction2 metabolite3

The real problem happens when you have more than two metabolites involved in the same reaction.  In that case, you need to make your reactions nodes (you can resize the nodes later so they "disappear").  Now your file should look something like:

metabolite1 reaction1 met reac
metabolite2 reaction1 met reac
metabolite1 reaction2 met reac
metabolite3 reaction2 met reac

Now the "met" column should be read in as a source node attribute and the "reac" column should be read in as a target node attribute.  This will allow you separately style the metabolites and reaction nodes.  By the way, if metabolite3 is a product of reaction2, you would probably write the last like as:

reaction2 metabolite3 reac met

that way you can use edge directions to show the directionality of the reaction.

-- scooter

 
On 04/27/2017 02:49 AM, Ankita Chatterjee wrote:

I am new to network analysis using Cytoscape. I have names of metabolites and their associated reactions. How to generate a metabolic network in which nodes represent the metabolites and edges represent reactions (So, if two metabolites participate in the same reaction, they should be connected by an edge representing the reaction/enzyme)? 

Thank you.

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[Ankita Chatterjee]

Hi Morris. 

Thank you for your suggestions. I was able to generate a network when only two metabolites are involved in a reaction (as an example). However, I have to work with a network with more than two metabolites involved in the same reaction. So, I followed your suggestion and created a sample file (Pls see the attachment). I think am making a mistake as am not being able to generate a network out of it when importing in cytoscape. Also, I do not want reactions to be represented as nodes. Reactions should be edges that represent connectivity between the metabolites. Kindly help. 

[Ankita Chatterjee]

On Thursday, April 27, 2017 at 3:19:14 PM UTC+5:30, Ankita Chatterjee wrote:

[Scooter Morris]

Here is what I get after importing your file:

I used the File->Import->Network->File and chose the first column as the source node, the second column as the target, the third column as source node attribute and the final column as a target node attribute.  Then I set up a discrete mapper for node size and I set the node size to 1 if the node was a reaction.  A little moving things around and I got the above.

-- scooter

[Ankita Chatterjee]

Hi Scooter

I followed the methodology as suggested by you and I could generate a network of the sample file. However, I have few queries: (1) I want the edges to represent reactions. Here, what we are doing is, making the reaction nodes disappear (by assigning node size 1) Thus, edges do not represent the reactions that are common for metabolites. The reaction names are getting overlapped along the edges and looking clumsy. Should it be the correct representation? (2) Do we need to assign node size individually to each reaction node manually? In my case the real network will have around 150 metabolites and 400 reactions.

Thanks again for your time!

On Thursday, April 27, 2017 at 3:19:14 PM UTC+5:30, Ankita Chatterjee wrote:

[Scooter Morris]

On 05/01/2017 03:01 AM, Ankita Chatterjee wrote:

Hi Scooter

I followed the methodology as suggested by you and I could generate a network of the sample file. However, I have few queries: (1) I want the edges to represent reactions. Here, what we are doing is, making the reaction nodes disappear (by assigning node size 1) Thus, edges do not represent the reactions that are common for metabolites.

I suppose that's technically true, but it's the best we can do.  Cytoscape doesn't support hypergraphs.

The reaction names are getting overlapped along the edges and looking clumsy. Should it be the correct representation?

There are lots of options for moving node labels around.  You may one to take a look at the node position options in the Style tab (look under Properties if you don't see it at first).

(2) Do we need to assign node size individually to each reaction node manually? In my case the real network will have around 150 metabolites and 400 reactions.

No, you can set up a mapping function in the Style tab that will map all nodes with "reac" to size 1.

Thanks again for your time!

-- scooter

On Thursday, April 27, 2017 at 3:19:14 PM UTC+5:30, Ankita Chatterjee wrote:

I am new to network analysis using Cytoscape. I have names of metabolites and their associated reactions. How to generate a metabolic network in which nodes represent the metabolites and edges represent reactions (So, if two metabolites participate in the same reaction, they should be connected by an edge representing the reaction/enzyme)? 

Thank you.

[Ankita Chatterjee]

Hello!

I am trying to assign colors to different sets of nodes at one go by using VizMap Discrete Mapping. I assigned separate attributes for the two sets of nodes (eg: Cor_1 and Colr_2).  For the first set of nodes this is working out. But as soon as I am selecting the second set of nodes, the first set of nodes which I had previously colored goes back to the old color. What can I do to resolve this?

Thanks.

Sincerely

Ankita Chatterjee

DST SERB NPDF

National Centre For Cell Sciences, Pune, India

On Mon, May 1, 2017 at 7:54 PM, Scooter Morris <sco...@cgl.ucsf.edu> wrote:

On 05/01/2017 03:01 AM, Ankita Chatterjee wrote:

Hi Scooter

I followed the methodology as suggested by you and I could generate a network of the sample file. However, I have few queries: (1) I want the edges to represent reactions. Here, what we are doing is, making the reaction nodes disappear (by assigning node size 1) Thus, edges do not represent the reactions that are common for metabolites.

I suppose that's technically true, but it's the best we can do.  Cytoscape doesn't support hypergraphs.

The reaction names are getting overlapped along the edges and looking clumsy. Should it be the correct representation?

There are lots of options for moving node labels around.  You may one to take a look at the node position options in the Style tab (look under Properties if you don't see it at first).

(2) Do we need to assign node size individually to each reaction node manually? In my case the real network will have around 150 metabolites and 400 reactions.

No, you can set up a mapping function in the Style tab that will map all nodes with "reac" to size 1.

Thanks again for your time!

-- scooter

On Thursday, April 27, 2017 at 3:19:14 PM UTC+5:30, Ankita Chatterjee wrote:

I am new to network analysis using Cytoscape. I have names of metabolites and their associated reactions. How to generate a metabolic network in which nodes represent the metabolites and edges represent reactions (So, if two metabolites participate in the same reaction, they should be connected by an edge representing the reaction/enzyme)? 

Thank you.

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[Matthias König]

Hi Ankita,
you could also simply encode your species-reaction graph in SBML and load the model with cy3sbml.
You have a node attribute type which you can use in your VisualMappings.
The example VisualMappings in cy3sbml make extensive use of it to display the species differently than the reactions.

Let me know if you need help encoding your graph in SBML.
There are very good libraries for that, namely
libsbml (c, c++, python, Java, R bindings)
jsbml (native java library)

The best
Matthias

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[Ankita Chatterjee]

Hello!

I am using cytoscape version 3.5.1. After assigning colors to nodes based on their degree, I want to assign different color to some selected nodes. In cytoscape 2.8.3 it was easily achievable (right click on the node and set color), but am unable to do the same in version 3.5.1.   Kindly help.

Thanks.

Sincerely

Ankita Chatterjee

DST SERB NPDF

National Centre For Cell Sciences, Pune, India

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[Ankita Chatterjee]

Oh I got it.. it can be done by selecting the bypass column under style section. 

😊

Sincerely

Ankita Chatterjee

DST SERB NPDF

National Centre For Cell Sciences, Pune, India

On Fri, Jul 14, 2017 at 11:42 AM, Ankita Chatterjee <bioinfo....@gmail.com> wrote:

Hello!

I am using cytoscape version 3.5.1. After assigning colors to nodes based on their degree, I want to assign different color to some selected nodes. In cytoscape 2.8.3 it was easily achievable (right click on the node and set color), but am unable to do the same in version 3.5.1.   Kindly help.

Thanks.

Sincerely

Ankita Chatterjee

DST SERB NPDF

National Centre For Cell Sciences, Pune, India

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[Ankita Chatterjee]

Hello!

For a network with 6 nodes and 10 interactions (for example) can we find the minimum number of nodes involved in only 10%, 20% (and so on) number of interactions. So, precisely, for this example I need to find how many nodes are involved when number of interactions are 1 (10% of total interactions), 2 (20%), 3 (30%) and so on. Can any of the network analysis parameters be used for this?

Thanks!

Sincerely

Ankita Chatterjee

DST SERB NPDF

National Centre For Cell Sciences, Pune, India

[Ankush Sharma]

Hi Ankita,

Degree distribution of networks will provide you number of interaction a node possess.  Hope it helps.

Best Regards,

​Ankush Sharma,PhD 

Bioinformatics Consultant - 

University of Miami,FL, U.S

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[Ankita Chatterjee]

Hi Ankush,

Degree distribution gives the relation between number of nodes and its degree. Though degree and interactions mean the same thing for each  node, but in totality number of interactions in a network is far more than the degree of each node. So, my question is how to plot a graph between number of nodes involved in 10%, 20% (so on..) of total interaction. For ex: if there are 10 interactions, then there could be 3 nodes involved in 4 out of 10 interactions and 6 nodes involved in remaining 6 out of 10 interactions. So, is there a way to plot this?

Thanks!

Sincerely

Ankita Chatterjee

DST SERB NPDF

National Centre For Cell Sciences, Pune, India

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[Ankita Chatterjee]

Hi!

I am using cytoscape 3.5.1. Which app can be used for cluster analysis? While trying to install MCODE or clusterMaker2.0, its showing that the apps cannot be installed since these are not compatible with the installed cytoscape version.  

Thank you!

Sincerely

Ankita Chatterjee

DST SERB NPDF

National Centre For Cell Sciences, Pune, India

On Wed, Jul 26, 2017 at 2:22 PM, Ankita Chatterjee <bioinfo....@gmail.com> wrote:

Ok, Thank you.

Sincerely

Ankita Chatterjee

DST SERB NPDF

National Centre For Cell Sciences, Pune, India

On Wed, Jul 26, 2017 at 1:32 PM, Ankush Sharma <ankus...@gmail.com> wrote:

Hi Ankita , 

I'm afraid that there is no app in cytoscape to do this.  Exporting data and using R or excel could be of use. 

Best regards 

Ankush Sharma 

Bioinformatics Consultant at University of Miami

CASyM (EU-FP7) Postdoctoral Research Associate 

Institute of Clinical Physiology, National Research Council of Italy, Siena ,Italy

 

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[Scooter Morris]

Hi Ankita,
    clusterMaker2 is certainly compatible with Cytoscape 3.5.1.  What version of Java and OS are you on?

-- scooter

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[Ankita Chatterjee]

Hi Scooter,

I am using Windows 7 (64 bit) and Java 7. Please see the attached screen shot of the error that I am getting.

Thank you.

Ankita 

Sincerely

Ankita Chatterjee

DST SERB NPDF

National Centre For Cell Sciences, Pune, India

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[piet molenaar]

Hi Ankita,

The app manager or webbased install should choose the appropriate version, how do you try to install the apps?

Best regards,

Piet

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

tel (+31) 20-5666592
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[Ankita Chatterjee]

Hi Piet,

I am trying to install it from http://apps.cytoscape.org/apps/clustermaker2. Please see the attached screen shot of the error that I am getting. I also tried to download the file, but I am getting the error as "this is a restricted site".

Thank You.

Sincerely

Ankita

Sincerely

Ankita Chatterjee

DST SERB NPDF

National Centre For Cell Sciences, Pune, India

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University of Amsterdam
Meibergdreef 9
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[piet molenaar]

Did you succeed in installing other apps in this way?

Can this be a firewall issue of some kind?

You can also try the app manager from within Cytoscape; Apps>App manager (http://manual.cytoscape.org/en/stable/App_Manager.html)

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[Barry Demchak]

Hi, all –

 

I don’t know what is up with this … I just tried this on my PC and had no problems of any sort.

 

Regardless, while we consider what could be going wrong, I’d like to make a copy of ClusterMaker2 available to Ankita here: http://chianti.ucsd.edu/~bdemchak/clusterMaker2-1.1.0.jar

 

Ankita … does this happen on any other PC? More information is helpful.

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[Barry Demchak]

Hi, Ankita –

 

Something’s wrong here … Windows 7/64 is OK for Cytoscape 3.5.1, but Java 7 is not. Cytoscape shouldn’t even start without Java 8. Would you mind verifying your Java version … on the Cytoscape splash screen (during startup) or on the Help | About panel.

 

Thanks.

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Ankita Chatterjee
Sent: Wednesday, August 09, 2017 11:06 PM
To: cytoscape...@googlegroups.com
Subject: Re: [cytoscape-helpdesk] Re: Generating metabolic network

 

Hi Scooter,

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[Ankita Chatterjee]

Hi all,

The problem got resolved once I updated the windows. :) 

Thanks for the suggestions!

Ankita

Sincerely

Ankita Chatterjee

DST SERB NPDF

National Centre For Cell Sciences, Pune, India

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