Importing miRNA expression data in PathVisio

[lmr...@gmail.com]

Hi,

I am seeking to visualize human miRNA expression data in PathVisio. For this purpose I have installed the latest version of PathVisio and the necessary databases, as well as the Regulatory Interaction Plugin. To begin with, I have loaded an interaction file (for the plugin) which contains miRNAs and their corresponding target genes. In this file, the regulatory elements consist in the miRNA ID (e.g., hsa-miR-222-3p). For these to be recognized during file loading, I have select the “mature miRNA sequence” as the system code for every line in the table and the file uploads with no problem. However, when I try to import miRNA expression data containing miRNA IDs, none of the identifiers is recognized. I have tried using MIMAT accession numbers instead but it does not work also. Which identifiers and/or system codes should I use so that PathVisio recognizes mature miRNA sequences in the expression data?

 

Thank you very much in advance.

Luís Vieira

[Luís Vieira]

Hi,

 

I am seeking to visualize human miRNA expression data in PathVisio. For this purpose I have installed the latest version of PathVisio and the necessary databases, as well as the Regulatory Interaction Plugin. To begin with, I have loaded the interaction file with the plugin which contains miRNAs and their corresponding target genes, along with other useful information (e.g. Pubmed ID) as a table format. In this file, the regulatory elements consist in the miRNA ID (e.g., hsa-miR-222-3p). For these to be recognized during file loading, I select the “mature miRNA sequence” as the system code for every line in the table and the file uploads with no problem. However, when I try to import my miRNA expression table in PathVisio containing miRNA IDs, it does not recognize any of the identifiers. I have tried using “miRNA sequence” as the system code instead  but it does not work also. How can PathVisio recognize mature miRNA sequences in the expression data?

 

Thank you very much in advance.

 

Best regards,

 

Luís Vieira

Coordenador da Unidade de Tecnologia e Inovação

Departamento de Genética Humana

INSTITUTO NACIONAL DE SAÚDE DOUTOR RICARDO JORGE

Avenida Padre Cruz, 1649-016 Lisboa, PORTUGAL

TEL +351 21 7526440 FAX +351 21 7526410

www.insa.pt

PENSE ANTES DE IMPRIMIR

 

 

 

[Alexander Pico]

Hi Luis,

I've found the miRNA identifiers to be very difficult to work with. PathVisio attempts to do some smart ID mapping as part of the import. This works when the identifiers in BridgeDb are clear (most cases), but I'm not surprised that it's tricky here.  Maybe someone else on this list has advice on how to do this in PathVisio... in the meantime, here is how I would do it.

Personally, I would try this in Cytoscape (cytoscape.org). With the WikiPathways App for Cytoscape, you can import pathways by WPID or keywords search and then you can extend them with miRNA target interactions and perform data mapping, looking at the ID types available (i.e., in the Table Panel). If you have never used Cytoscape before, this might take a while to learn a new tool, so I don't want to give the false impression that this is easy.  But you are trying to do something that is difficult...  Here's a tutorial: https://cytoscape.org/cytoscape-tutorials/protocols/wikipathways-app/#/title

I can also recommend our PathwayFinder tool, which takes IDs like hsa-miR-222-3p and identifies pathways with TARGETS of those miRNAs using "strong functional" evidence from miRTarBase, e.g., https://www.wikipathways.org/wpi/extensions/PathwayFinder/?identifiers=hsa-miR-222-3p. You can enter lists of miRNA and update the search results. This can help you identify which pathways to import into Cytoscape, for example. 

Hope this helps, 

 - Alex