GO terms

[@MrRamaeri]

thank you so much for your presentation. God bless you

[@George-rq1yp]

Excellent! You know how to explain stuff!

[@hengzhao308]

Th!is is a wonderful series of teaching about gene expression analysis! Thank you so much, Mike!

[@muratseker6406]

thank you for the videos they are quite helpful

[@muratseker6406]

for some reason I come across your channel by chance. KZbin algoritms were not helpful

[@jems6840]

Thank you for this wonderful tutorial. I do have a question though : When I run GO analysis for my upregulated DEGs ( p < 0.05), 99% of the GO terms associated with specific genes have padjusted value greater than 0.05 and a lot of them have pvalue of 1 , Why does this happen? If I am interested in a Gene X in a treatment group that is differentially upregulated but the GO terms have p-value > 0.05 how do I interpret it ?

[@mikevandewege3007]

So your genes may be upregulated, but there may not be any specific functions or pathways that are biased among upregulated genes. The adjusted p-value corrects for multiple tests. A p-value of 0.05 still means 5% of tests will be significant by chance, sooo we try to filter out the most likely false positives. Hope that helps.

[@khanmohdsarim8211]

After StringTie I have locus tag and read count, which I have used for Deseq2, Kindly inform me how to convert these Locus tag to gene id because Panther database is not recognizing Locus tag ID and giving all unmapped result. Thanks

[@PhanCanhTrinhPlus]

Hi Mike, I am trying to use Panther for Klebsiella pneumoniae with my protein list. Is it possible to use for K. pneumoniae. I tried many time but I cannot get any result. Please help me if you know. Thank you very much! (example ID: M7PZH9 M7QKV7 M7PNJ0 M7QE19 M7PB39 M7PY01 M7P355 M7QCU5 )

[@alessiaartusi5233]

Hi, is there some package or function to plot the results?

[@mikevandewege3007]

For those results specifically, not really. However, I have used an R package (clusterProfiler) that helps make nice enrichment plots.

[@ds5375]

To save you 34 minutes. This video does NOT show you how to download and parse the files.

[@nitinshukla999]

mike I need more tutorials videos .. what next from here. please update

[@mikevandewege3007]

Recognize this was all just for my bioinformatics class during covid that i'm leaving up. I really have no intention of making new videos. Were you looking for anything specific?

[@lidiaryabova]

@@mikevandewege3007 Dear Mike, I found your explanation really really good .If you pan to do something , please make video on gene annotation with different methods please ..

[@saravalero6679]

why if I introduce 20 genes, there are 20000 results??

[@vishweshbharadiya6758]

Oh mann no statistically significant results uhhhh 😫😫