Thanks for this presentation.

@asifmolbio

7 ай бұрын

Glad you like it

Thanks, it has resolved so many questions I was having

@asifmolbio

3 ай бұрын

Glad if its helpful

very nice explaination

@asifmolbio

29 күн бұрын

Glad you like it

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

@asifmolbio

Жыл бұрын

Glad it helping.

@emmafiallos2972

Жыл бұрын

@@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

Жыл бұрын

I never tried, but i will have try on this

@emmafiallos2972

Жыл бұрын

@@asifmolbio thanks Dr

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

Жыл бұрын

Glad you like it

@deeptirao5982

Жыл бұрын

Is this the right way sir?

@asifmolbio

Жыл бұрын

You can send your analysis reports on asifalikalas@foxmail.com

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

8 ай бұрын

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

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

Жыл бұрын

With all

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

8 ай бұрын

yes separatly uploading would have more clear interpretation.

@sangitapaul6463

8 ай бұрын

@@asifmolbio thank you so much for this suggestion

@sangitapaul6463

8 ай бұрын

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

@asifmolbio

8 ай бұрын

Glad if it’s helping

@sangitapaul6463

8 ай бұрын

@@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?

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

29 күн бұрын

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

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

10 ай бұрын

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

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

@asifmolbio

4 ай бұрын

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

Thanks so much. I still have some questions

@asifmolbio

8 ай бұрын

?

@adekunleajiboye1244

8 ай бұрын

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

@asifmolbio

8 ай бұрын

It depends on your phenotype and literature reported

@asifmolbio

8 ай бұрын

How to select genes for qPCR validation in transcriptome/RNA seq data? kzread.info/dash/bejne/goacqqScmq6ne7g.html

@adekunleajiboye1244

8 ай бұрын

@@asifmolbio Thanks so much Dr.

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

8 ай бұрын

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

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

@asifmolbio

Жыл бұрын

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

@researcher7410

Жыл бұрын

@@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

Жыл бұрын

@@researcher7410 please send me your file asifalikalas@foxmail.com i will reply you after weekend

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

2 ай бұрын

Check excel file by yourself hopefully this video will be helpful

@asifmolbio

2 ай бұрын

How to calculate FC, log2FC, Pvalue, Padj, Up/down genes in RNA seq data using Excel kzread.info/dash/bejne/enxnr86lZLqbh6g.html

@DiyahNoviSekarini

2 ай бұрын

@@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

2 ай бұрын

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

@DiyahNoviSekarini

2 ай бұрын

@@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?

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

@asifmolbio

3 ай бұрын

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

@asifmolbio

3 ай бұрын

Welcome

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

Жыл бұрын

Highest in negative would be most significant

@asifmolbio

Жыл бұрын

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

@asifmolbio

Жыл бұрын

Wslam

@Bihar2Korea

Жыл бұрын

Sukriya Sir... Thank you Sir

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

@asifmolbio

4 ай бұрын

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

@Fashionastic

4 ай бұрын

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

@Fashionastic

4 ай бұрын

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

@asifmolbio

4 ай бұрын

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

4 ай бұрын

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

p̷r̷o̷m̷o̷s̷m̷ ☹️

thank u but I didnt get the whole concepts

@asifmolbio

4 ай бұрын

Have you previously watched some videos about transcriptome sequencing