miRNA Network construction and analysis

Question

[Soltani]

Hello !

I want to do a construction and analysis of regulatory genetic networks in specific disease based on involved microRNAs, target genes and transcription factors

Please can you inform me about free tools that can help me to build and analyze a miRNA/Target genes/TFs network.

Thank you in advance.

Answer 1

[Sasha Fokin]

We are now building a database and online dataviz tool on cytoscape web -- MirOB (MicroRNA OncoBase).

Database includes validated microRNAs and Transcription Factors Targets associated with human cancers. Currently, MirOB supports only homo sapiens organism.

Network shows all interactions containing transcription factor of miRNA.

You can try our simple tool here.

[Sasha Fokin]

If you looking for chronic myeloid leukemia, i open simple network for this disease: http://mirob.interactome.ru/_____gene_network_TefzK8tA (but in our database only about 30 validated TF-miRNA-TF interactions associated with CML)

Answer 2

[Chris Evelo]

You could try our CyTargetLinker.

CyTargetLinker is an app (plugin) for the network tool Cytoscape. It is available from the Cytoscape App Store (for free, in case that might suggest otherwise, it is also Open Source).

CyTargetlinker was described in PLoS One and the project site is here.

CyTargetLinker allows you to extend a network with information from resources that are loaded as "Regulatory Interaction Networks" (RegINs). RegINs for transcription factor and miRNA targets from various sources, including Encode, are available for download. You will probably want to use it in combination with the BridgeDb app to make sure you get the identifier mapping right.

Answer 3

[Soltani]

I'm extremely grateful for you answering my question! I just want to know if I can use it in the case of extending my network with other gene lists i.e miRNAs host genes, TcoFs (transcription cofactors)! If it is possible,how to make it please?

[Chris Evelo]

If you want to comment on an answer please put it as such and not as a new answer to your question.

For miRNA host genes the solution I described should already work. You can add miRNA to the network and originating database (and the BridgeDb mapping databases) should know where that miRNA comes from.

If you want to work with more complicated transcription factor complexes than the ones described in the resources covered in the current RegINs (TFe and ENCODE for human), you would have to find the resource you want to use and to create your own RegIN.

[Soltani]

Thank you for your help! CyTargetLinker seems to be the best way to solve my problem

[Soltani]

Hello, you must forgive my ignorance Sir, I tried to create my own RegIN from Transmir database But I couldn't do it all alone. Is there a tutorial or a detailed way to do it please ?! (I tried to follow the tutorial on the website but I could not get a result).Thank you in advance!