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13.11.15

Version 2.1 - We have a fantastic new tool to visialise the drug interactions within the esyN networks. Now gives your favourite human interaction network - discover which drugs bind to it.
We are using the drug - target interactions from DrugBank:

Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J.
DrugBank: a comprehensive resource for in silico drug discovery and exploration.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D668-72. 16381955

Drug repurposing and combination are two very hot areas in drug discovery. At esyN we have developed a new tool that allows you to visualise which drugs are known to bind to proteins in your interaction network. This tool, in combination with all other features of esyN makes it dramatically easier for any user to study, build and analyse biological interaction networks.

Start with a list of your favourite genes, add them in the "Network from list" link on the right hand side of the esyN graphs tool. Choose a database you want to stream the data from and choose what type of interactions (i.e. genetic and/or physical) and esyN will produce a graph for you. Now - if your network is for H. sapiens you will probably want to add the drug interactions. Go to the bottom of the page - under Advanced tools (Interactions tab), choose the H. sapiens - Drugbank and then click the "Fill" button. This will add to the network all the known drugs that interact with any protein in your network.

11.11.15: Network Disruption

What does it mean "Network Disruption" ?
Given a network between various entities (genes and proteins in the case of www.esyn.org) which nodes should I delete to disrupt the network as quickly as possible?
There are many excellent recent studies on this subject in particular [1,2] where they investigate which algorithm is best to achieve such a goal. In [1] the authors conclude that using betweenness with a sequential target attack is best, that is, given a network, calculate the most central node using the betweenness centrality, remove that node and re-calculate the betweenness and restart the cycle. In [2] the authors introduce a new algorithm, the collective influence, which supposedly does better although there is no direct comparison with the results in [1].
In esyN (www.esyn.org) we have implemented both ways allowing the users to apply a number of different algorithms to calculate the most central nodes and then remove these genes from the next calculation and see how the network properties change without that central gene. For example if we try to destroy the central component (157 genes) of the network:
http://www.esyn.org/builder.php?publishedid=294&type=Graph
Using the betweenness centrality with a sequential targeted attack as described in [1] we notice that just in 10 steps after deleting the genes: TSG101, EXOC7, EXOC2, RINT1, SNAP23, VAMP2, ARF1, SNAP29, KIAA0196, FAM21A the largest connected component goes from 157 to 46 genes.

Publish

Using the Collective Influence with radius 2 after deleting 10 genes:  TSG101, EXOC7, EXOC2, PDCD6IP, SNAP23, VAMP2, SNAP29, NUP50, CCDC93, VPS51 the largest connected component goes from 157 to 118 genes.

Publish

References
1. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0059613
2. http://www.nature.com/nature/journal/v524/n7563/full/nature14604.html



30.09.15

Version 2.0 - You can now start analysing your networks in esyN. Choose between Degree, Closeness, Betweenness, Eccentricity, Radiality, Stress, Centroid Value and Collective Influence centralities. By selecting "Distrupt the Network" option you can simulate the effect of deleting one or more nodes on the value of these centralities. This new type of analysis is crucial inportance when planning a to perturb the network either with an inhibiting drug or with a knock out (or RNAi) experiment. We have also added the ability to calculate and visualise the shortest path between any two nodes in the network.

23.07.15

New updates and bug fixes

19.04.15

Version 1.95 - Retrieve interactions directly from HumanMine, MouseMine and YeastMine!

21.01.15

Version 1.9 Released! Now it is possible to embed an esyN network in any HTML page. Read the documentation or visit your favourite network and click the "Generate embed link" at the bottom of the graph area and follow the instructions.

08.12.14

Version 1.8 Released! We have added the choice between high and low throughput when downloading the interactions from BioGRID and we have fixed a number of small bugs.

24.11.14

Version 1.7 reselased! We have added the experimental details of the interactions and fixed some other minor details

13.11.14

Version 1.6 reselased! In the Browse page - the networks are now organised in some broad categories (All networs, Neurodegeneration, H. sapiens, Model Organisms) - more will follow. We have also added the feature to disable the editing mode - so it will be easier to browse networks without unexpectedly adding nodes.

11.11.14

Version 1.5 reselased! Now its possible to automatically create a Graph from a list of genes.

06.11.14

Version 1.4 reselased. We have added the ability to search for interactions in many other organisms, the force directed layout, and we have added a direct link to our issues page in Bitbucket, so that anybody can let us know of any problems.

02.09.14

esyN - manuscript published:

PLoS ONE 9(9): e106035. (2014)

10.07.14

Version 1.3 reselased. We have added the ability to search node names in ensembl and updated the FAQs

15.05.14

Version 1.2 reselased. We have added new functionalities to the Explore page such as the search for nodes and the ability to sort the results according to project name, author name or publication date.

26.04.14

Version 1.1 released. We have added extra functionalities in the publishing tool. New features include the ability to add a description and 5 tags in each published network, and search among all the networks.

18.03.14

Version 1.0 of esyN released! We wellcome your suggestions and inputs. Please contact us at: info@esyn.org

12.03.14

We Thank Carlo Pirchio for his help in styling our esyN logo