Gene ontology : GO and KEGG enrichment analysis | Shiny GO

[@momaz4143]

Many thanks for this, one question please. all of these methods are showing over-representative because of a treatment (for example) but how about if a gene get under-representative because of a treatment?

[@asifmolbio]

Both possibilities (up and down) can be visualized, In video which part you are talking about tell me in minutes and seconds

[@momaz4143]

@@asifmolbio how down can be visulized in GO? negtive fold chnage? or negative like biological function? can you give an example how a negtive GO can be persented in your platform,please. thanks

[@asifmolbio]

Oh now i got your question, GO shiny tool is only used to check enrichment it means whatever a list of genes we entered, the functions of those genes were related to which gene ontology (category). To check up and down you need to use iDEP tool 0.95 please see there a video about this tool on my channel

[@tolerakeno3948]

Today I asked my roommate "Asad" that what is enrichment and kegg pathway analysis . And he recommended me to check your channel for the lecture about this. I am really impressed the way you explained and teaching. Thank you so much. Keep it up

[@asifmolbio]

Keno, pay my regards to him. I am glad if these videos are helping you. Stay in touch

[@AlonKedem1000]

For bioinformatic its the best video in the world

[@asifmolbio]

Glad you like it

[@Kaleem.a.q]

As usual am The first one who ever watched it yet...... Mjy bio matric m hi bht ajeeb lgti the.....r ab B's video m picsture Dekhi......wording py kan nahi dhry .😂😂😂😂😄😄😄😄

[@hassankarim9451]

Very informative and helpful for my analysis. Thanks a lot

[@asifmolbio]

Glad it was helpful!

[@sreeram6416]

Sir in shiny go what is meant by pathway size please clear it for me sir

[@thirumoorthy1894]

Best information

[@keepcalm414]

Thanks for this video

[@asifmolbio]

Most welcome

[@hamasatmohammed2616]

Thanks for the informative video sir, i have a concern... i have different genes sets for different bacterial isolates and when i want to choose the species i can not find them and also for the KEGG pathway this option is not available for my bacteria

[@asifmolbio]

Yes some species are not available in this

[@sunitabista3096]

Amazing video

[@Mzalendo2295]

Very informative, thank you.

[@asifmolbio]

Glad you like it

[@ankitthakur950]

It is very informative video but if you could explain that what different functionalities represnt then that will be much better, link what can we conclute by or what are things reprensenting in the graph.

[@asifmolbio]

doi.org/10.3390/ijms23147887

[@asifmolbio]

Please read the attached paper all details have here

[@grsbiosciences]

Sir please explain what is gene ontology and gene enrichment analysis. What we conclude from these

[@asifmolbio]

This is database to annotate the genes. This part of transcriptome analysis. Alot of literature is available in google

[@stalina6504]

sir i have doubts example if im going to do some reseacrh on cancer where can i get the gene for running shinygo?

[@asifmolbio]

Usually you get these genes from company, which you sent for analysis of RNA seq

[@husnainahmad4749]

what about if our species genome (citrus grandis) is not available at this website?

[@asifmolbio]

Its the limitation of GO shiny. Use NCBI compatible ids and not select any specie while performing. Check if it works

[@AlexOotzaAkaSharpy]

Can you please PLEASE PLEASE do the iDEP tutorial, I really need it for my project I will be working with RNA-seq data! Thank you very much, kind sir. I love your videos!

[@asifmolbio]

Please stay tuned, will upload soon

[@asifmolbio]

RNA Seq data analysis with webtool | IDEP | Transcriptome analysis Link>>kzbin.info/www/bejne/bKSxqoGPfcSpaLc kzbin.info/www/bejne/bKSxqoGPfcSpaLc

[@safirullah5635]

excellent job

[@asifmolbio]

Thanks

[@momaz4143]

in KEGG how can i find which pathway is the best ? there are few pathways and I am not sure which one is better? there is no nGene or fold chnage.... thanks

[@asifmolbio]

Download list of genes, that pathways which have lowest values of P value ( for example 10 power -07) is your pathway, you can use them (few top with lowest p values) for final explanation

[@samkhan7536]

very informative

[@asifmolbio]

Its great if you like it

[@user-kj8xf9xl5v]

The input only contains the name of Genes, where did the Enrichment FDR, Fold enrichment comes from?

[@asifmolbio]

You can try iDEP tool.

[@user-kj8xf9xl5v]

@@asifmolbio Thanks for your reply. I think my question is in the GOshiny web tool, I only saw you input a list of genes without other info (like value, FDR, or FC), but your result from the GOshiny seems to have Enrichment FDR, and Fold enrichment values. So I was curious about where this value comes from?

[@asifmolbio]

In GO shiny tool, enrichment is calculated based on probability of a given GO function ( BP, CC, MF) for a given set of genes/data. P values and FDR is also based on predictive models.

[@aftabahmad4867]

can we do enrichment analysis for sequences which are not submitted to any public database? if I want to check enrichment for genome, or genes from my local database, not submitted to any database, so no accession of gene I.d number, what should I do in that case ? please guide..

[@asifmolbio]

Unfortunately GO shiny is not suitable for those species which are not submitted in public databases

[@enriquep4857]

Is it possible to use this if i have protein ID from uniprot instead of genes names?

[@asifmolbio]

Yes it is

[@joannagouliou2644]

I cannot understand why the -log10 (FDR) value is most of the times so high. Αs the FDR value is suggested to be 0.05 - 0,1 in order for the results to be consistent, how can we explain this kind of -log FDR value (e.g 20 , 30 ect)? Thank you in advance sir!

[@asifmolbio]

I agree with your point, can you send your results tables or screenshots (with high fdr) and criteria you choose while filtering to me by email [e-mail]

[@joannagouliou2644]

@@asifmolbio Thank you! I sent them.

[@momaz4143]

and please what is the diference between "STRING" and "Netwrok" in your platfrom? thanks,

[@asifmolbio]

String is the name software which creates interaction and network is the final form of interactions

[@momaz4143]

@@asifmolbio Many thanks, do you mind please explain how fold enrichment is computed in your pltform, if fold enrichment is relative calulation?

[@asifmolbio]

Fold enrichment is a simple ratio of expression between control and treatment. Lets suppose in control expression: 5 reads In treatment expression: 15 reads Fold enrichment would be: 15/5=3 It simply mean expression of this genes is three fold more enriched in treatment compared to control

[@mahjabeenmahjabeen1137]

Hi, will we be able to obtain KEGG pathways just for 8-10 select genes !?

[@asifmolbio]

You can try

[@mahjabeenmahjabeen1137]

@@asifmolbio I tried but, not able to do so

[@asifmolbio]

Which is your specie mske sure your ID format is ok

[@avinafisa4711]

great!keep it up

[@asifmolbio]

Thank you, I will

[@marwatawfik3956]

Thanks. Is it preferable to run each of down and up regulated gene list seperately?

[@asifmolbio]

No need of separate

[@marwatawfik3956]

@@asifmolbio Thanks again. so the enriched output is considered up regualted or down regulated if my comparisoin is B vs A?

[@RahulSk-sp4zy]

thank you very much, sir, this video is very helpful for me. Sir, do you have a video for a related gene search?

[@asifmolbio]

kzbin.info/www/bejne/gpaxm6ahl6triLs

[@MB-vd6hc]

Thanks for the video; I uploaded a set of genes all features are working except the KEGG, this option is not in the left side menu; do you have any idea about it?

[@asifmolbio]

First select GO category. Go biological functions, cellular component or molecular functions then try

[@shandanaaali7498]

Asslam o alikum Sir your videos are really helpful for us in proteiomic database analysis thank you so much for uploading such valuable videos for us..... Sir I have a problem when I would like to upload gene accession in SHINY GO ....it show IDs not recognised........I get the accession ID from the Perseus please guide me how to upload the gene ID

[@asifmolbio]

Thanks, Please change your accessions IDs corresponding to NCBI. Sometimes local databases IDs are not indentified by SHINY GO and iDEP.

[@husnainahmad4749]

can we do gene ontology annotation by using NCBI gene IDs?

[@asifmolbio]

Yes Gene ID not recognized problem: Gene ontology enrichment analysis using GO shiny tool kzbin.info/www/bejne/m5Oze5KagZemqdU

[@nurulnadzirah298]

sir, what paper do you use in 9.17 mins. Can you provide the link to that paper? TQ

[@asifmolbio]

www.biorxiv.org/content/biorxiv/suppl/2018/05/04/315150.DC1/315150-1.pdf

[@vinitha2774]

Very Informative.. Sir, I have a some queries about enrichment analysis. I have collected list of genes related to some disorders from literature review. I want to do enrichment analysis for the selected genes. In shiny go tool, I got the results for my selected genes. And my question is, I did enrichment analysis for single gene set only, is this correct way to do that?

[@asifmolbio]

Yes you can

[@vinitha2774]

@@asifmolbio Thank you for your response.

[@researcher7410]

How to extract list of gene from GFF file because there are few genes which are not annotated by their name. sir could you please tell me how to do that part?

[@asifmolbio]

i will upload a video how to solve the problems of id not recongnized. stay tuned

[@JourneyGrowthHub]

Sir g I am having an experiment on the role of the lignin metabolic pathway in drought stress tolernce. Can you guide me in some steps?

[@asifmolbio]

It depends what you have already done, and what’s remaining share your complete plan or ppt with me by email: [e-mail]

[@wpzhddd5212]

Very imformative sir, but i try to change ' # of top pathways to show' category, then change all enrichment score and chart image. In this case, what dose it mean?

[@asifmolbio]

I couldn’t understand you properly , however if you will change the number of top pathways off course chart and images will be updated accordingly

[@riteshchandra6073]

How to download this gene list.

[@asifmolbio]

*www.biorxiv.org/content/biorxiv/suppl/2018/05/04/315150.DC1/315150-1.pdf see table 2. as an example or you can use your own gene list from SRA database or

[@riteshchandra6073]

Actually sir I have complete knowledge about others ontology but I don't idea about gene ontology but your video motivate me regarding gene ontology , but how I download the list of this gene for enrichment analysis.

[@riteshchandra6073]

@@asifmolbio ok i will check thanks for your support and help.

[@asifmolbio]

@@riteshchandra6073 please look up in table 2 in the mentioned link

[@aviksarkar6138]

Sir, In New shiny GO 0.77 version KEGG pathway option is not there in the pathway database, please make a new video for these version

[@asifmolbio]

Dear Avik, thanks for message. I will make a new video soon

[@aviksarkar6138]

@@asifmolbio Thank you Sir...

[@deeptirao5982]

We are giving only gene names as input, how does it calculate FC, p-value, etc. Please explain.

[@asifmolbio]

Dear Deepti, please be informed that one gene has many annotated functions. Each gene is mostly assigned to many ontologies. Given a set of gene ontologies FC level of more prevailed Biological processes, cellular components, and Molecular functions can be calculated. however, if you want the comparison of two treatments we should use the iDEP tool.

[@deeptirao5982]

@@asifmolbio oh okay sir. But that takes me to another doubt. If something shows a FC of 10, then with respect to what is the fold change 10 times, since there could be 5 GOs attached to the gene. Shouldn't there be multiple FC values for all the possible GO comparisons?

[@asifmolbio]

@@deeptirao5982 These are just hypergeometric tests and help us calculate how likely the enrichment is by chance (in the case of FDR or P value), while the fold enrichment is an estimation of the percentage of genes in your list compared to the background selected. If each gene has many functions so these tests can tell us which to believe and which to reject. if one gene has many annotated functions each one is already calculated separately with a different name. in other words, it means each gene can be contributing to more than one/too many pathways at a time.

[@DilawarAbbasPhD]

Kindly make a Video on how to use statistics 8.1 software

[@asifmolbio]

Thanks stay tuned , will upload a video about this

[@DilawarAbbasPhD]

@@asifmolbio thanks 😊

[@vijeta9495]

After clicking on KEGG it shows diagram downloading can take 3 minutes but not getting the diagram. Please help me out

[@asifmolbio]

Can you change to good internet, i never faced this issue.

[@vijeta9495]

@@asifmolbio But i m not facing the same problem when doing with demo genes on same system and same internet connection

[@asifmolbio]

Can you send your screenshot of problem and list of genes to me at [e-mail]

[@vijeta9495]

@@asifmolbio Please check your mail id

[@samvedkulkarni4705]

Hi sir, I had a question. I have created a chart using the available genes. How can I calculate the area of the circles representing the number of genes?

[@asifmolbio]

You don’t have legend along your main figure to compare gene number ?

[@sg4024]

Great video Sir.Thanks a lot! What to do if we have a list of proteins and want to see protein ontology?Please guide.

[@asifmolbio]

You can try with proteins ID hopefully it will work

[@sg4024]

@@asifmolbio Yes Sir.Thank u!.It worked.But it is not showing if all the proteins got annotated or only some. I gave a list of 555 proteins but I am not able to identify which ones got annotated and which ones belong to which pathway.

[@swarnadabral]

Sir, can you please explain what is fold enrichment?

[@asifmolbio]

Lets suppose expression of a gene in condition 1 is seven time higher than conditions 2. It means it is 7 fold (up) enrichment in condition 1 compared to that of 2.

[@ayeshawadoodwadood5679]

V. informative. Sir I have a question. i tried to perform GO enrichment analysis. but i encountered with one problem. some of the gene ids are not covered. and when i saw "Genes" option in this software, few genes were mentioned as "not mapped" . so how to handle this problem?

[@asifmolbio]

Try to switch those genes IDs with other databases like ensemble, NCBI or phytozome

[@ayeshawadoodwadood5679]

@@asifmolbio i am using NCBI database. while ensembl plant is not working.

[@asifmolbio]

NCBI is also fine, unfortunately this version has some shortcomings. A new version is under way, which will be released soon and will integrate few more IDs successfully. Hope so

[@ayeshawadoodwadood5679]

@@asifmolbio Thank you

[@chusman7195]

Amazing sir, Its very informative. keep it up, Sir , could you please make a video or if you have a video then can you share for plants, GO and KEGG analysis for genome wide gene family genes, so how can we predict their GO and KEGG pathways, as well as Molecular, Biological and Cellular functions etc, Thanks a lot sir, Looking forward

[@asifmolbio]

kzbin.info/www/bejne/bKSxqoGPfcSpaLc

[@asifmolbio]

Please see this video it’s related

[@chusman7195]

@@asifmolbio Thank you very much sir, I have watched that video also, so in that video used the known genes such and predict their annotations, what in case of Gene family ? so we have to use the reference genes name for next analysis or how?

[@zohairaqayyum4143]

Will this tool used to ontology of miRNA as well?

[@asifmolbio]

yes it can be used for miRNAs gene ontology but you need to use gene IDs rather than name of genes.

[@zohairaqayyum4143]

@@asifmolbio Thank You

[@zohairaqayyum4143]

@@asifmolbio is NCBI accession number accepted here or not?

[@asifmolbio]

@@zohairaqayyum4143 not accession number of NCBI, but gene ID given in NCBI database can be accepted

[@zohairaqayyum4143]

@@asifmolbio ya right Thank You Sir.

[@charmyshah8944]

Hi, so can I use this for microarray data that I got for DEG from GEOdatasets?

[@asifmolbio]

Yes you can use

[@nusrathfathima3471]

Can we paste protein unimportant ID here

[@asifmolbio]

Protein unimportant or protein uniprot ID?

[@nusrathfathima3471]

@@asifmolbio yes , Uniprot ID of protein profiling data of control and disease

[@asifmolbio]

Technically It should work, you can have a try

[@nusrathfathima3471]

@@asifmolbio Got results ..but unable to get Kegg and Iam not sure whether the IDs control vs patient is corrector not

[@nusrathfathima3471]

@@asifmolbio Sir, I drop email we will discuss further their .

[@muhammadanees2008]

My desire specie database is not available , could you please tell us that how can we specie database?

[@asifmolbio]

Yes some species are not available, you can use it by default search, and no need to select any specie

[@muhammadanees2008]

@@asifmolbio Thank you!

[@sanjaisrao484]

Thanks

[@asifmolbio]

Glad you like it

[@raminderkaur6263]

Hi sir, can we use it for Triticum aestivum?

[@asifmolbio]

Yes can

[@trishitabose2228]

Excuseme sir -The site is not at all working the way you did give another webserver

[@asifmolbio]

Are you using vpn

[@asifmolbio]

I have checked Go shiny version 0.80 is working without any vpn

[@trishitabose2228]

What is vpn sir?

[@trishitabose2228]

@@asifmolbio i tried all versions still i got 0 response, its showing reconnecting like that.

[@asifmolbio]

From which country you are trying to access? Can you change internet i am sure its working

[@israr2547]

ISRARUL HAQUE

[@snehaunni194]

Sir i just start work on transcriptome analysis.. All the vedios related to this are useful for students like me. If we hav any query or douts can u provide ur mail id or number to contact u sir

[@asifmolbio]

Thanks sneha, you can post your questions in-comments here or contact me at [e-mail]

[@snehaunni194]

@@asifmolbio Thank you very much sir