How to write and interpret gene ontology (GO) in research articles ?

#howtowrite #geneontology #researcharticle
In this video, I have demonstrated how to write and interpret the results of gene ontology (GO) analysis.
gene ontology
gene ontology enrichment analysis
gene ontology tutorial
gene ontology analysis
differentially expressed genes in r
gene ontology how to use
differentially expressed genes
research
gene annotation
gene ontology (go) enrichment analysis
gene ontology annotation
gene expression
how to write paper in urdu/hinid whole transcriptome rna sequencing
ontology
introduction to rna-seq
gene set enrichment
gene set enrichment analysis
what is gene ontology

[@usmanali3520]

very nice explaination

[@asifmolbio]

Glad you like it

[@dorcasojo3501]

Thanks for this presentation.

[@asifmolbio]

Glad you like it

[@gsgamerz4665]

Thanks, it has resolved so many questions I was having

[@asifmolbio]

Glad if its helpful

[@emmafiallos2972]

Thanks for sharing with us all these valuable information. I have learned interesting things for applying in my PhD.

[@asifmolbio]

Glad it helping.

[@emmafiallos2972]

@@asifmolbio have you ever used WeGO ?? I would like to know how uses it. It's like ShinyGO. I have been researching tutorials about WeGo but I have not found them yet.

[@asifmolbio]

I never tried, but i will have try on this

[@emmafiallos2972]

@@asifmolbio thanks Dr

[@deeptirao5982]

Very nicely explained sir. Thanks! I have listed out the lowest nodes and generated bubble plot for enrichment, to be more specific with my analysis. Please comment on this.

[@asifmolbio]

Glad you like it

[@deeptirao5982]

Is this the right way sir?

[@asifmolbio]

You can send your analysis reports on [e-mail]

[@amanullahbaloch332]

Thanks for sharing valuable information. Could you please guide me. I have total 5 lines and 1 control total 6 lines. For each i have Go term individually. Can i write result for each one by one? Data is analyzed by analysist they did not provide combined result and did not mentioned upregulated or down regulated GO term, same in KEGG .

[@asifmolbio]

Combined results are better or explain on your best performance treatment vs control in detail

[@user-ub9qm5ip3c]

Thanks for the video. My original research plan was to study the effect of omega-3 fatty acids on inflammation and antioxidant genes but based on what I have in my differentially expressed genes, none of the common genes associated with inflammation and oxidative stress are found. What should I do?

[@asifmolbio]

Might be few genes have indirect association. You need to check top DEGs for their function and annotation. They must have relationships with your phenotype under study

[@sangitapaul6463]

Your presentations are really helpful! Can you please suggest me that for my proteomics data if i want to prepare this gene ontology and enrichment analysis, do i need to run the downregulated proteins and the upregulated ones separately? As in this video you talked only about the 10 downregulated ones.

[@asifmolbio]

yes separatly uploading would have more clear interpretation.

[@sangitapaul6463]

@@asifmolbio thank you so much for this suggestion

[@sangitapaul6463]

Your suggestion worked so well for me..thank you brother..I am really thankful to you.

[@asifmolbio]

Glad if it’s helping

[@sangitapaul6463]

@@asifmolbio brother can you please tell me..that what does the y axis denotes in any of the bar plot or dot plots in gene enrichment analysis..in my data the name of the particular enriched components are written in the y axis..and x axis denoted with enrichment score with -log10 p value. Is it like this, that the highest significant component gets the topmost position in the y axis?

[@enriquep4857]

Thank you for your video. But have 1100 DEGs, should a do the GO with only the 30 more significant? Why i can't use all?

[@asifmolbio]

With all

[@nedafiroz514]

How can we interpret the go excel file for rna seq data to find genes responsible for stress or depression? I need to find them from go excel file and write them in my research paper for my assignment

[@asifmolbio]

Try to use GO shiny tool and perform motif sequence analysis to identify transcription factor

[@adekunleajiboye1244]

Thanks for the Video Dr. Please what's your full name? I would love to read some of your papers so as to know how to interpret and write my paper

[@asifmolbio]

You can write Asif Ali, Sichuan Agricultural University on google to search me

[@user-uz4sk5cr6v]

how can i know if theses genes were down or up- regulated in a specific phenotype?

[@asifmolbio]

Please check the company should have sent you list down and up regulated genes in the excel list.

[@researcher7410]

How to perform GO enrichment analysis on genomic data???? Sir can you please tell me...

[@asifmolbio]

If genomic data is in the form of genes. Off course you can perform GO enrichment analysis.

[@researcher7410]

@@asifmolbio ... Yes.... I have an annotations file of genes and proteins but i don't know how to do this GO enrichment analysis?? Could you please elaborate?

[@asifmolbio]

@@researcher7410 please send me your file [e-mail] i will reply you after weekend

[@vysakhvg4137]

Sir in my treatment 12000 genes up regulated is this much big number is okay? And it is statistically significant

[@asifmolbio]

If 12000 passes significance criteria log fc > 2 and p value

[@asifmolbio]

Welcome

[@DiyahNoviSekarini]

Hello Dr. Asif, I would like to ask that I do get the GO analysis with webgestalt without upregulated and down regulated gene information, how can I decided which gene that coding the up/down regulation of webgestalt GO analysis result? Thankyou

[@asifmolbio]

Check excel file by yourself hopefully this video will be helpful

[@asifmolbio]

How to calculate FC, log2FC, Pvalue, Padj, Up/down genes in RNA seq data using Excel kzbin.info/www/bejne/fnmWfp-iabxojac

[@DiyahNoviSekarini]

@@asifmolbio well noted, but I do confused where to find the number in the control and treatment's column? because i just find the gene information through swiss target prediction and using interactivenn, and sometimes i use the david analysis to find the p-value.

[@asifmolbio]

@@DiyahNoviSekarini you dont have any excel list for your transcriptome data?

[@DiyahNoviSekarini]

@@asifmolbio No, I dont, I just do in silico and got the result from the STRING, David, ShinyGO, and Webgestalt. Is there any method to interpret the upregulated/downregulated based on these?

[@adekunleajiboye1244]

Thanks so much. I still have some questions

[@asifmolbio]

?

[@adekunleajiboye1244]

Please which pathway analysis do you recommend I use for the analysis?

[@asifmolbio]

It depends on your phenotype and literature reported

[@asifmolbio]

How to select genes for qPCR validation in transcriptome/RNA seq data? kzbin.info/www/bejne/hoPLeXWZn7B0gbc

[@adekunleajiboye1244]

@@asifmolbio Thanks so much Dr.

[@Bihar2Korea]

Asalamualaikum...sir FAQ no.1 Sir why you called p value highest for significant..... I think if p value less than 0.05 then it is significant... next question. Why we log 10p value.. Explain Sir please

[@asifmolbio]

Highest in negative would be most significant

[@asifmolbio]

We represent p value in log 10 for easy representation like .000000015258 is better or 1.5*10power 9

[@asifmolbio]

Wslam

[@Bihar2Korea]

Sukriya Sir... Thank you Sir

[@prof.drasmaam.salihalmohai9983]

thank u but I didnt get the whole concepts

[@asifmolbio]

Have you previously watched some videos about transcriptome sequencing

[@Fashionastic]

Sir i want your help to complete my project... I'm stuck in a step that is gene ontology.. Please help me out

[@asifmolbio]

please let me know about your questions in comments i will help you

[@Fashionastic]

@@asifmolbio I'm doing a project which is related to genistein and its target for making network

[@Fashionastic]

@@asifmolbio I want to perform gene ontology and kegg pathway analysis of some genes

[@asifmolbio]

Have you done some analysis? Have you found interacting partners from literature? Interaction obtained through networks are not reliable until tested through experiments like Y2H & BiFC

[@Fashionastic]

@@asifmolbio I don't have guide sir.. I myself performed this by watching KZbin video and not able to perform it perfectly

[@alexanderdeanna5839]

p̷r̷o̷m̷o̷s̷m̷ ☹️