How to annotate edgeR results?

Question

[Balatheskulter]

I have got log2fold change by using edgeR.

geneID        logFC         logCPM       PValue
AG1IA_00007   0.457824277   6.711014893  8.44E-53
AG1IA_00008   1.514709777   4.376560603  3.28E-111
AG1IA_00009   -0.409884055  5.357685435  1.39E-19
AG1IA_00010   0.36806713    4.554970223  5.85E-10
AG1IA_00011   -0.338575977  1.144437033  0.095242116

I needed to functional annotate this table. This belongs to fungi (Rhizoctonia solani), I also have gtf and gff files.. can anyone help me by giving commands to annotate this.

[jared.andrews07]

What do you mean by "functionally annotate"? What information are you trying to add? Can you give an example of your desired output?

[Balatheskulter]

geneID logFC logCPM PValue product

AG1IA_00007 0.457824277 6.711014893 8.44E-53 vesicular-fusion protein SEC18

AG1IA_00008 1.514709777 4.376560603 3.28E-111 hypothetical protein AG1IA_00008

AG1IA_00009 -0.409884055 5.357685435 1.39E-19 ran binding protein 11

AG1IA_00010 0.36806713 4.554970223 5.85E-10 peroxisomal biogenesis factor 2

AG1IA_00011 -0.338575977 1.144437033 0.095242116 hypothetical protein AG1IA_00011

I needed to functional annotate this last row(product).

I have got these names by individually copy-pasting the gene names in NCBI. There are 10538 genes, I can't do this manually ... so I need some help Jared.andrews.

[cschu181]

There is a genome sequence and gene annotation for that fungus available here. Maybe redo your analysis to use those data. Alternatively, you can do ORF prediction/translation on your transcripts and annotate using HMMer, blastp, or interproscan.

Answer 1

[h.mon]

The annotation is available at the Rice Sheath Blight Pathogen Genomics Database download page (here). You then have to format the gene set of interest into some format the functional enrichment software you want to use - for example, here is a list of formats Broad GSEA accepts: Data formats.