Connect gene names to GO terms/function for loading in DESeq2

Question

[Moneeb Bajwa]

Hi,

I would like to connect the gene names to GO terms and function before loading them into DESeq2. The counts are from single-end mouse reads mapped to the genome and annotation files from GENCODE.

The counts files I have look like this right now:

   gene_id               counts     gene_name
1 ENSMUSG00000064842.1      0       Gm26206
2 ENSMUSG00000051951.5      4          Xkr4
3 ENSMUSG00000102851.1      0 RP23-317L18.1
4 ENSMUSG00000103377.1      0 RP23-317L18.4
5 ENSMUSG00000104017.1      0 RP23-317L18.3
6 ENSMUSG00000103025.1      0  RP23-115I1.6

I intend on making a graph similar to Figure D in this link (taken from the paper that performed this study already): http://cancerres.aacrjournals.org/content/canres/78/5/1334/F5.large.jpg. This is their full paper: http://cancerres.aacrjournals.org/content/78/5/1334

Not sure what to do. I appreciate the help.

Answer 1

[Prakash]

In Figure D , what they have shown is enriched GO terms for 363 AKT differentially expressed genes. GO terms and DESeq2 analysis are two different things. you can find enriched GO terms for whole set of gene but that would be very less meaningful. I would rather first go for differential expression analysis using DESeq2 and then do GO term enrichment analysis.

Thanks

[Moneeb Bajwa]

Thank you. But how would I get the GO annotations for that? I tried a couple websites like https://go.princeton.edu/cgi-bin/GOTermFinder but I don't understand why it doesn't give me any results? I just put like RP23-115I1.6 and select mouse genome it should return something right? It didn't work.

[Prakash]

The link you tried will only provide enriched GO terms for you set of genes, basically it compares your set of genes against respective databases and calculates enrichment and significance. providing only one gene will not return anything. If you really interested in only GO annotation, then you should try biomaRt R package or just download GO annotation file extract GO ID