Pathway Grouping with Genes

Question

[aggie]

I want to group (cluster) given gene names according to pathway knowledge. How can I do this and which package should I use in R ?

Answer 1

[EagleEye]

JFI: Also we must be aware of how often these tools are updating their databases (I am not talking about KEGGREST, it is about other available tools for functional enrichment analysis). Otherwise the information we get from these tools might be misleading.

These articles explains the problems associated with outdated source.

GeneSCF: a real-time based functional enrichment tool with support for multiple organisms

Nature methods, correspodence Impact of outdated gene annotations on pathway enrichment analysis

Complete article from the same author in bioRxiv Impact of knowledge accumulation on pathway enrichment analysis

Also checkout this link

[Persistent LABS]

Agreed that the database content has to be updated. Thanks for sharing this latest paper.

Answer 2

[EagleEye]

There is an linux based real-time tool GeneSCF, (Not R)

Gene Set Clustering based on Functional annotation (GeneSCF)

Answer 3

[Persistent LABS]

You can explore KEGGREST . Also if you are looking for online tools, you can explore WEB-based GEne SeT AnaLysis Toolkit for pathway analysis and clustering.

Thanks

Priyabrata

Persistent LABS