g:Profiler for Gene-Set Enrichment Analysis

[@inciek]

Hi Saniye, it is a great video and helps a lot. I could not figure it out: when I look into a detailed Excel file, there is a highlighted area, True and False. What does it mean? Should I consider True one or both? Because some GO shows False, and it includes my looking pathway. Thanks

[@marinaorphanidou1225]

Hi! thanks for this video! I don't understand the difference in the sources' results (GO, KEGG, HP, etc). Are the sources just different "platforms" and the results are shared information from those? And are the results just where these genes have their effects?

[@SaniyaKhullar]

Hi Marina, thanks for reaching out. The sources are basically databases for genes that focus on different aspects. We can look at a gene in many different ways. Even GO has 3 key parts: Cellular Components (CC), Biological Processes (BP), Molecular Functions (MF). While CC associates genes with parts of a cell, BP focuses on associating genes with pathways that take place, and MF is associating genes with molecular Functions. Human Phenotype Ontology (HP) associates abnormalities in genes with potential phenotypes and diseases that are observed. There are so many data sources and gene lists. Please let me know if you have further questions and please do subscribe to my channel for more updates and videos on this content.

[@koterm]

Hi Saniya, VERY helpful video, thank you very much! All the best! :-)

[@SaniyaKhullar]

Hi Marek, I am so happy that you found this video to be very helpful!! Thanks for subscribing as well and for your nice wishes :-)

[@kaisakaiho725]

Thank you for the useful content!

[@SaniyaKhullar]

Thank you Kaisa!! I am so happy it helped you! Please do subscribe to my channel for more content. :)

[@yugankchaudhary1691]

That GESA presentation using gprofiler was great, can you give another presentation on comparison analysis using gprofiler

[@SaniyaKhullar]

Thanks Yugank! I really appreciate your kind feedback and I will certainly make such a presentation. Please subscribe and stay tuned :)

[@rishimaborah9956]

You have beautiful cats!😊❣

[@SaniyaKhullar]

Thank you so much Rishima!! Please do subscribe and see other videos with these cute cats (Yangqi cat and Mei cat) :)

[@rishimaborah9956]

@@SaniyaKhullar Sure!:)

[@chriz5492]

That's nice presentation, appreciated, could you please make a video for the cellular, biologicals, molecular function annotation prediction in plants using the genome wide identification of gene family , At the same time could you make and share some videos for Transcriptomic data analysis using raw data from NCBI and generate the FPKM and lOG FC using Ubunto or other easy program, Thanks a lot looking forward

[@SaniyaKhullar]

Hi Ch Riz, thanks for your kind words and for your helpful suggestions on additional videos! I have made some more on gProfiler and will be uploading those. I also will try to make videos based on what you have suggested and will keep you posted. Please do subscribe for more updates :)

[@jimmywong4615]

very helpful for my lab report! thank you very much!

[@SaniyaKhullar]

Thank you Jimmy for your feedback!! I am so happy it helped you with your report and I hope my videos can help you more work in the future!!

[@katherinotalora6071]

Hi thanks for the video, one question, if I put a listing with the GO codes, for example: GO:0006511 in the g:GOST section, will it be ok? My result is millions of GO MF, BP....

[@SaniyaKhullar]

Hi Katherin, I am so sorry for the delay. I do not think you could input in gene GO codes there. Please note I do have a playlist of videos for g:Profiler tools (kzbin.info/aero/PL_3UUp3wcnVaiWRnoKqh3BBDxVXXmLee2). Please do check that out and let me know if that answers any questions. Please do subscribe for more updates :)

[@rishimaborah9956]

Do you know how to remove SNPs that have MAF lower than 5%?

[@SaniyaKhullar]

Hi Rishima, please do check out this video of mine on using R to do this kzbin.info/www/bejne/o5rYnJ94oKaIrrM. I talk about getting the MAF for SNPs there, which you can use for filtering. I have other introductory videos on downloading R and Bioconductor and getting started. Please let me know if this helps.

[@hmmmumm8183]

thank you so much.

[@SaniyaKhullar]

I am happy this helped Hmm Mumm. Please do subscribe for more updates. I have a new playlist for gprofiler.

[@juliettec7173]

hey! thank you for the video! do you know if we can also use gProfiler for gene set enrichment analysis of circular and long non coding RNAs? :)

[@SaniyaKhullar]

Hi Juliette, I'm so happy to help! I tried the tool for lncRNAs and it was not so good, unfortunately. However, I did find a tool (rpubs.com/golgun/649085) called NoRCE in Bioconductor that could help with such enrichments for non-coding RNA enrichment (based on this paper: bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04112-9#availability-of-data-and-materials). I can try to create a video walking through this as well. Please do subscribe for more updates :)

[@juliettec7173]

@@SaniyaKhullar Hi Saniya, thank you so much for your reply! I heard about using Bioconductor too, but I am not really familiar with using R. If you could make a video about this, that would be super helpful and highly appreciated! :)

[@SaniyaKhullar]

@@juliettec7173 that sounds great. I'll try to do this as soon as possible :). I have videos on bioconductor and R on my channel.

[@SaniyaKhullar]

@@juliettec7173 Hi Juliette, I found a really nice tool for long non-coding RNA analysis and have prepared a video (with you in mind) on using this tool for gaining more insights. Please see: kzbin.info/www/bejne/ppuuaX6XjamoepI

[@mahanthivasu859]

ma'am can i get your gmail id?

[@SaniyaKhullar]

Hi Mahanthi, apologies for the delay. Please do see my profile page and the about section for more details. In any case, I hope my video helped. Please do subscribe and reach out with any more questions :)