Help with creating my own .gmt file (Gene Set)

[Francesca De Faveri]

Hi,

i am trying to create a custom gene set to use on my GSEA analysis on Staphylococcus aureus with GSEAPreRanked (with mac). However, I've tried creating my own .gmt  file in R with Pathway as first column, description as second, and list of genes (each gene in a different cell of the same pathway row) and it doesnt show up on the local GMT/GMX section of GSEA. I have downloaded as .tab from R and then converted into .gmt but it doesnt seem to work. I have submitted my gene set to gsea...@broadinstitute.org. 

I would greatly appreciate it if I can get some help regarding this! 

[Francesca De Faveri]

--
You received this message because you are subscribed to a topic in the Google Groups "gsea-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/gsea-help/4Vp5PxV5RG0/unsubscribe.
To unsubscribe from this group and all its topics, send an email to gsea-help+...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/gsea-help/7000d985-42be-498c-ba92-d6f9a080570fn%40googlegroups.com.

[Anthony Castanza]

Hi Francesca,

Happy to try to help you with this. I see a couple things with the file, first that it is using a .tab file extension when in order to be parsed by GSEA, it needs to use one of our file formats, in this case, .gmt should be correct: https://docs.gsea-msigdb.org/#GSEA/Data_Formats/#gmt-gene-matrix-transposed-file-format-gmt

However, there are a couple other issue with respect to compliance with that extension's expected format. Here are the first couple examples from the file you sent for reference:

Pathway Description 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73

PWY-8086 "(<i>S</i>)-lactate fermentation to propanoate, acetate and hydrogen" SAUSA300_RS09855 SAUSA300_RS05645 SAUSA300_RS08995 SAUSA300_RS05455 SAUSA300_RS14075 SAUSA300_RS01250 SAUSA300_RS01155 SAUSA300_RS03050 SAUSA300_RS09045 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

PWY-5837 "1,4-dihydroxy-2-naphthoate biosynthesis" SAUSA300_RS09500 SAUSA300_RS09495 SAUSA300_RS05080 SAUSA300_RS05085 SAUSA300_RS05090 SAUSA300_RS05095 SAUSA300_RS06770 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

PWY-7180 "2-deoxy-&alpha;-D-ribose 1-phosphate degradation" SAUSA300_RS00740 SAUSA300_RS11515 SAUSA300_RS00735 SAUSA300_RS00800 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

PWY-8121 "2-deoxy-D-glucose 6-phosphate degradation" SAUSA300_RS14255 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

PWY-5084 "2-oxoglutarate decarboxylation to succinyl-CoA" SAUSA300_RS07100 SAUSA300_RS05365 SAUSA300_RS08010 SAUSA300_RS07105 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

PWY-5046 "2-oxoisovalerate decarboxylation to isobutanoyl-CoA" SAUSA300_RS05355 SAUSA300_RS05365 SAUSA300_RS08010 SAUSA300_RS08000 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

Firstly, that header row should be removed, this specification doesn't support a header.

Secondly, the filler NA's need to be stripped, this is probably a missing flag from the write command you used to produce the file.

Lastly, the long and complex descriptions in the second column; I am not confident that these will be properly parsed with all the special characters. I would try to strip them down if possible, or omit them if not, when R auto-quotes output like that, it is generally because of possible breaking characters, and this may be of concern with GSEA's parsing code.

If you continue to encounter difficulties with preparing your datafile, or run into additional errors when loading it, or attempting to analyze data with it, please let us know

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Sanford Burnham Prebys Medical Discovery Institute

---

From: gsea...@googlegroups.com <gsea...@googlegroups.com> on behalf of Francesca De Faveri <francescad...@gmail.com>
Sent: Tuesday, July 21, 2026 12:11 AM
To: gsea...@googlegroups.com <gsea...@googlegroups.com>
Subject: Re: [gsea-help] Help with creating my own .gmt file (Gene Set)

 

[EXTERNAL EMAIL: This message may not be safe, use caution, and please be suspicious of any attachments contained in this email.]

You don't often get email from francescad...@gmail.com. Learn why this is important

You received this message because you are subscribed to the Google Groups "gsea-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gsea-help+...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/gsea-help/CANwVWfRDydGe7DJtOZvHeFvxvBi1vXqjgyVpn7%3DQnZs1LT3gyQ%40mail.gmail.com.