Tutorial on how to map list of Ensembl IDs?

[Veronica Urbik]

Hello!

I am hoping to import a list of Ensembl gene IDs (about 500), and then be able to match the genes to the pathways that they are in. I do not want to draw my own pathways, but simply be able to identify where these genes already appear in existing pathways. Does anyone have experience doing something like this? I downloaded the wikipathways homosapien files, as well as the Hs_Derby_Ensembl files for the bridgedb plugin. I am looking for instructions or a tutorial of some sort, as I am not sure if I am on the right path. Thank you very much! 

[Kristina Hanspers]

Hi Veronica,

I’m assuming the 500 genes are considered of interested somehow (differentially expressed?). To find pathways of interest, here are two options:

1. Load your full dataset (not just the 500 genes) into PathVisio (https://www.pathvisio.org/), and then use the “Statistics” feature (with the WikiPathways archive loaded) to find interesting pathways. For example, if you filtered your dataset based on some parameter (p-value etc) to get the list of 500, you setup the same criteria in the Statistics interface. You can see an example workflow here: https://www.pathvisio.org/documentation/tutorials/tutorial-2/

2. Use a third-party tool that incorporates WikiPathways content, directly on the list of 500. For example, Enrichr (http://amp.pharm.mssm.edu/Enrichr/) takes a list of genes and performs over-representation analysis against WikiPathways, GO and many other libraries. Once you have a list of pathways, you can open those in PathVisio, load your data and visualize it on the pathways.

Hope this helps,

Regards,

Kristina

On Jun 22, 2018, at 2:36 PM, 'Veronica Urbik' via wikipathways-discuss <wikipathwa...@googlegroups.com> wrote:

Hello!

I am hoping to import a list of Ensembl gene IDs (about 500), and then be able to match the genes to the pathways that they are in. I do not want to draw my own pathways, but simply be able to identify where these genes already appear in existing pathways. Does anyone have experience doing something like this? I downloaded the wikipathways homosapien files, as well as the Hs_Derby_Ensembl files for the bridgedb plugin. I am looking for instructions or a tutorial of some sort, as I am not sure if I am on the right path. Thank you very much! 

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