Analysis ideas for a list of DEG with a lot of unannotated regions?

Question

[hakimelakhrass]

As the title states I have a list of DEGs I want do some sort of functional and path way analysis. As of now my only option has been removing unannotated regions. This is from microarray data so with probe IDs I can get to a BED file that has coordinates. What kind of analysis can I do that includes the unannotated regions to possibly see if they have link to my annotated genes or to maybe get at their functions. Thanks

Answer 1

[biocyberman]

Please provide some minimal example of input and output data. It's still not clear to me what you want to achieve. Lacking that information, I can only think of these two well-written tutorials:

http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html (Region to gene annotation)

http://www.bioconductor.org/packages/release/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html (Gene to pathway annotation)

[hakimelakhrass]

Okay so what I have is microarray data. I use limma to get a list of differentially expressed genes. The thing is SO many of them exist in unannotated regions. I have the data about the coordinates so I can make a BED file. Which means even though I have no information about the gene I know where it exists. So I want to do now some sort of analysis to make sense of my data. Up until know I have been removing the NAs and just using the ranked gene list in Genemania and String.db.

Now I want to incorporate these unannotated regions in some sort of analysis but idk how.