How to perform gene enrichment (GO and KEGG pathways) analysis with SR plot

#howto #enrichment #kegg #SRplot
In this video, I have performed gene enrichment analysis gene ontology, and KEGG pathway using SR online web tool.
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[@herieldavidmauki6327]

Thanks so much for introducing to some of us who did not know this website tool before. You are a genius and a hero🎉🎉🎉❤

[@asifmolbio]

Glad if its helping the community around

[@Muuip]

Thank you! Much appreciated!👍

[@asifmolbio]

You’re welcome

[@cynthiapaztrejo5245]

This video save me… it gives you a very good analysis. Your videos are very informative.

[@asifmolbio]

Glad you like it

[@Dr.MuddasarSaeed]

Thanks again very informative ❤

[@asifmolbio]

Glad you like it

[@natalyurshanski8031]

Thank you, it is very useful!

[@asifmolbio]

Glad if it’s helping

[@azharshahansha5174]

Sir, I have a request to make a elaborate video for creating cluster of orthologous groups of proteins(COG) using bacterial wholegenome sequence

[@asifmolbio]

Sure, i have added your topic for future videos please stay tuned

[@Khanbadoshiyan]

Thanks for this nice explanation, but what if I have non-model bacterial data and it is not on the list. I wanted to perform GO and especially Gene Set Enrichment Analysis, but there is no Org.db package in the database, and its KEGG database is also not available for the majority of genes, I am extremely interested to perform GSEA. Can you please suggest or make vedio on how can someone create .gmt file, cls, etc file for using non-model organisms for Broad Institute GSEA or through the cluster profiler?

[@asifmolbio]

Please check iDEP and Go shiny tool videos on my channel. You can use them for your intended analyses

[@rpj4130]

Fantastic! I hava a question: Are you choosing positive values ​​because you are only interested in seeing overexpressed genes or can this analysis only be done with positive values ​​and not combine them? Thank you..

[@asifmolbio]

It can be done with both positive and negative values

[@MohammadSalehi-bt4qs]

Thank you for the information. I want to perform gene enrichment analysis, gene ontology, and KEGG pathway for less-known non-coding RNAs called tRNA-derived fragments, but I can't figure out how. Researchers have attempted to analyze the existing literature, but I am unsure of how to conduct the analysis myself. Unfortunately, the website you suggested was also unable to retrieve the desired results.

[@asifmolbio]

Thanks for message, what was the error?

[@gautamnisha7193]

Dear sir very nice explanation. Can you please make one video on how to make volcano plots for selected gene set.

[@asifmolbio]

Sure stay tuned

[@samikshasaluja7978]

Greetings sir... thank you for uploading these informative and easily understandable videos. I request you to kindly provide information on how to perform gene enrichment analysis for plants (chickpea specificlly) also. This particular online tool is for animals only.

[@asifmolbio]

You can try go shiny tool or iDEP that is usable for both plants and animals

[@asifmolbio]

Videos are already uploaded.

[@mosihlamokumo5859]

What other software can I use if i have non-model species such as Zostera capensis (seagrass)?

[@asifmolbio]

You can email to arminstrator of iDEP tool. They will assign you a module for non-sequenced genomes.

[@osmanaksoy9862]

Thanks Asif for your helpful video. I have a list of target genes and I wanted to perform GO and KEGG pathways analysis but nothing came out. My list of genes does not contain FC values and the list is from chip-atlas dataset. How can i analyse it? I would be grateful if you help. Thanks.

[@asifmolbio]

You can try GO shiny tool and its video is available on my channel

[@azkacha_]

your videos are really good and easy to do. but why when I try to find the KEGG, CC, MF, and BP with SR Plot, Shiny Go, and manually in String db to excel: all the data is completely different. Do you have any recommendations which platform has more accurate results?

[@asifmolbio]

Yes right each has different algorithms and datasets for mapping which results in different results, all ate fine but probably SR plot is best

[@nahuelcesattilaluce1257]

thanks! Unfortunatelly my microarray returned me a lot more than 3k of DEGs... I find it little bit strange that the input limit is 3k of lines, when omics analysis are characterized by long set of data! Do you know any another option with a greater limit of gene inputs? Thanks again!

[@asifmolbio]

Can you try DAVID (Database for Annotation, Visualization, and Integrated Discovery) or Clusterprofiler?

[@ratihrinendyaputri6841]

Thank you, my question is where we can find FC value ?

[@asifmolbio]

The company analyst, who will perform transcriptome analysis will be providing excel files.

[@Leonie-Carolina]

Thank you for this video. Do you know if there is an option of entering my own specific reference gene list instead of just selecting the species? Thank you for your help!

[@asifmolbio]

Yes it can be used for your own gene list

[@Leonie-Carolina]

Thank you! Can you quickly explain where I enter my own reference list?

[@asifmolbio]

@@Leonie-Carolina you can enter this website there are several options for gene enrichment (which you can search through search tab) and try each one and download example and see and use that one which have list of genes

[@tadakunioscartam24]

Hi, how can u get the fold change if u the list from Kegg with only the IDs?

[@asifmolbio]

Retrieved from excel list of transcriptome data

[@Su.arya31]

Since we are getting different plots for same gens , can you suggest which plots graph we should include for our papers ?

[@asifmolbio]

Anyone of them you like can be used

[@rpj4130]

How dependable is it to rely on web-based tools for this analysis? In contrast to utilizing a UNIX system, where we have access to the algorithm and can tailor it for enhanced analytical control, as well as for conducting large-scale data analysis. Similarly, can we trust the analysis when only a few databases are examined? Thanks for your videos.

[@asifmolbio]

It is totally fine to rely on this tool as it also based on R, even script can be downloaded, however if someone has expertise in UNIX systems it has more options. This web tools is handy for those who are not into coding etc.

[@sudhanshumishra132]

How did you get the FC values of those genes?

[@asifmolbio]

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

[@user-bo6lw7yk1t]

Hi bro, can you please share any tool to perform gene enrichment (GO and KEGG) for yeast Saccharomyces cerevisiae dataset?

[@asifmolbio]

Try GO shiny tool

[@user-bo6lw7yk1t]

GO shinny tool is not working for RNA seq. Is there any other good tool?@@asifmolbio

[@asifmolbio]

iDEP

[@ChristinaCSkodra]

yes only for specific organisms though...and no plants, even for Arabidopsis...

[@asifmolbio]

Yes unfortunately not available for many. But why don’t you try iDEP tool and do this whole through webtool, it can process IDs from Arabidopsis

[@tanmoychatterjee7922]

Sir there is term present over sr plot website that is point. How to tackle this point problem. Please reply

[@asifmolbio]

What you mean by term ?

[@herieldavidmauki6327]

I have a question, what is the difference between GO terms and pathways? for instance what is difference between a certain biological process (GO term BP) and pathways? what do these two phenomena explain in the biological system? Thank you very much

[@asifmolbio]

Simple, as one pathway can have many genes to make a final product (protein). Similarly one gene can have more than one GO terms to predict their biological function.

[@herieldavidmauki6327]

​@@asifmolbio well elaborative professor. Could you kindly provide us with your contact details to easily reach out on you for collaborative projects in future?

[@asifmolbio]

Please write me at [e-mail]

[@herieldavidmauki6327]

​@@asifmolbio Thanks, I will

[@nimeshbhardwaj8666]

where we can find FC values of genes??

[@asifmolbio]

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

[@tanmoychatterjee7922]

Can I perform it without fc?? Please reply

[@asifmolbio]

Then you have to choose another format of graph you can go to bioinformatics.com.cn/en and check if any kegg has an option without fc

[@ayazahmad1245]

Sir, can we use the same process for proteomics data?

[@asifmolbio]

Yes can

[@mahjabeenmahjabeen1137]

Can we compare subtypes of any cancer!?

[@asifmolbio]

If have RNA seq data then can

[@aarshisrivastava5358]

How to calculate fc value ?

[@asifmolbio]

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

[@PrimoVascularSystem]

Thank you so much. i have a question. The data entered is only the gene name and FC value , how do you know the count and p-value data in the bubble chart.

[@asifmolbio]

The company should have already sent you count and P values. If you dont have you can use iDEP tool

[@asifmolbio]

RNA Seq / Transcriptome data analysis with a webtool | iDEP tool kzbin.info/www/bejne/bKSxqoGPfcSpaLc

[@PrimoVascularSystem]

The only data entered in this KZbin video is the genetic name and FC value, and I wonder how the count and p-value value appear in the bubble chart.

[@asifmolbio]

P value can also be estimated from FC value only

[@PrimoVascularSystem]

@@asifmolbio Thank you for your kind explanation. Could you provide me with a video or study that I can know the p-value with the fc value?

[@user-er8gz3ds3r]

sirt If I do have no FC value then what we do If I have Gene and FDR vale or P value then we show the GO plot? plz kindly reply to me, sir

[@asifmolbio]

To use shiny GO tool you only need gene IDs

[@asifmolbio]

How to create a KEGG pathway summary plot? kzbin.info/www/bejne/pmOxhXV4f9ifibM

[@The_Backpacker_Botanist]

I AM UNABLE TO PERFORM THIS AS I AM WORKING ON PLANT , BUT IN THE REFERENSE SPECIES SECTION THERE IS NO PLANT SPECIES. HELP ME IN THIS

[@asifmolbio]

How to avoid common errors/problems in SR plot data analysis tool? kzbin.info/www/bejne/inOWdGudZ7V5etE

[@asifmolbio]

Check this

[@user-hf1lk8ou3c]

What about corrected pvalues

[@asifmolbio]

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

[@asifmolbio]

Here is how to calculate

[@nusrathfathima3471]

File showing empty After download What could be the reason sir.

[@asifmolbio]

Try with a few genes first

[@nusrathfathima3471]

@@asifmolbio Tried sir. Unprotected and Fold change values Still not shoeing anything in results sir. Only on text document downloaed in file and it's showing there is no results.

[@esha6221]

or tell me about enrichment score

[@asifmolbio]

Number of genes in specific pathway/ total number of genes in all pathways

[@jujajuja742]

I am trying to submit but it is giving me a 403 error or a "servers are busy". Is there a way around this?

[@asifmolbio]

Can you try in a while or try with not too big data

[@jujajuja742]

@@asifmolbio I am using less genes and now I am getting this 3, use point as decimal separator, not comma. e.g. 3.14, not 3,14 as pi. None of my data uses commas

[@asifmolbio]

I think there is error in your formatting please have a look again on your data including column titles

[@jujajuja742]

@@asifmolbio If there is a formatting error I have no idea what it is. The columns are just gene name and logfc

[@jujajuja742]

Nvm I got the results thank you

[@tanmoychatterjee7922]

Sir how to interpret the results. Can you help. By making a video

[@asifmolbio]

How to interpret the results of KEGG pathway analysis? kzbin.info/www/bejne/o5a3eJmCi6eciNU

[@asifmolbio]

Its already uploaded check this 👉

[@tanmoychatterjee7922]

Ok sir. After a few times I will upload the actual issue with sr plot

[@esha6221]

sir what is p value

[@asifmolbio]

In pathway enrichment analysis, the p-value indicates the statistical significance of the enrichment of a particular biological pathway among a set of genes or proteins. It helps determine whether the observed enrichment is likely due to chance or if it reflects a true biological relationship. A low p-value suggests that the pathway is significantly enriched, meaning that the genes or proteins in the pathway are more likely to be associated with the experimental condition being studied.

[@samkhan7536]

Pentose phasphate pathway in may Transciptomic data... but I don't understand that... how to explain that

[@asifmolbio]

A putative SUBTILISIN-LIKE SERINE PROTEASE 1 (SUBSrP1) regulates anther cuticle biosynthesis and panicle development in rice

[@asifmolbio]

Read results of this article hopefully it would be helpful.

[@samkhan7536]

thanks ... I will

[@ashakumari4690]

Where is the negatively regulated or down regulated gene in these plots?

[@asifmolbio]

See the FC values

[@ashakumari4690]

@@asifmolbio If comparing two groups A (treated) with B (control) . I put both neg( downregulated ) in A and pos ( upregulated) in A, FC values as you suggested , but in the the graph the enrichment show only from 0 to pos direction. so genes which are neg or down in A are considered or not ? if yes there should enrichment beyond 0 toward neg as well for downregulated genes. or it is just considering upregulated gene or just using gene list we are uploading. please explain

[@asifmolbio]

You should upload the whole list together, not only up or down separately.

[@ashakumari4690]

yes sir i am uploading whole list which consist up and down both. @@asifmolbio