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?
@asifmolbio2 жыл бұрын
Both possibilities (up and down) can be visualized, In video which part you are talking about tell me in minutes and seconds
@momaz41432 жыл бұрын
@@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
@asifmolbio2 жыл бұрын
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 Жыл бұрын
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 Жыл бұрын
Keno, pay my regards to him. I am glad if these videos are helping you. Stay in touch
@AlonKedem10002 жыл бұрын
For bioinformatic its the best video in the world
@asifmolbio2 жыл бұрын
Glad you like it
@Kaleem.a.q2 жыл бұрын
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 .😂😂😂😂😄😄😄😄
@hassankarim94512 жыл бұрын
Very informative and helpful for my analysis. Thanks a lot
@asifmolbio2 жыл бұрын
Glad it was helpful!
@sreeram6416Ай бұрын
Sir in shiny go what is meant by pathway size please clear it for me sir
@thirumoorthy18942 жыл бұрын
Best information
@keepcalm4142 жыл бұрын
Thanks for this video
@asifmolbio2 жыл бұрын
Most welcome
@hamasatmohammed2616Ай бұрын
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
@asifmolbioАй бұрын
Yes some species are not available in this
@sunitabista30962 жыл бұрын
Amazing video
@Mzalendo22952 жыл бұрын
Very informative, thank you.
@asifmolbio2 жыл бұрын
Glad you like it
@ankitthakur950 Жыл бұрын
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 Жыл бұрын
doi.org/10.3390/ijms23147887
@asifmolbio Жыл бұрын
Please read the attached paper all details have here
@grsbiosciences2 жыл бұрын
Sir please explain what is gene ontology and gene enrichment analysis. What we conclude from these
@asifmolbio2 жыл бұрын
This is database to annotate the genes. This part of transcriptome analysis. Alot of literature is available in google
@stalina65048 ай бұрын
sir i have doubts example if im going to do some reseacrh on cancer where can i get the gene for running shinygo?
@asifmolbio8 ай бұрын
Usually you get these genes from company, which you sent for analysis of RNA seq
@husnainahmad4749 Жыл бұрын
what about if our species genome (citrus grandis) is not available at this website?
@asifmolbio Жыл бұрын
Its the limitation of GO shiny. Use NCBI compatible ids and not select any specie while performing. Check if it works
@AlexOotzaAkaSharpy2 жыл бұрын
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!
@asifmolbio2 жыл бұрын
Please stay tuned, will upload soon
@asifmolbio2 жыл бұрын
RNA Seq data analysis with webtool | IDEP | Transcriptome analysis Link>>kzbin.info/www/bejne/bKSxqoGPfcSpaLc kzbin.info/www/bejne/bKSxqoGPfcSpaLc
@safirullah56352 жыл бұрын
excellent job
@asifmolbio2 жыл бұрын
Thanks
@momaz41432 жыл бұрын
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
@asifmolbio2 жыл бұрын
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
@samkhan75362 жыл бұрын
very informative
@asifmolbio2 жыл бұрын
Its great if you like it
@user-kj8xf9xl5v Жыл бұрын
The input only contains the name of Genes, where did the Enrichment FDR, Fold enrichment comes from?
@asifmolbio Жыл бұрын
You can try iDEP tool.
@user-kj8xf9xl5v Жыл бұрын
@@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 Жыл бұрын
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.
@aftabahmad48672 жыл бұрын
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..
@asifmolbio2 жыл бұрын
Unfortunately GO shiny is not suitable for those species which are not submitted in public databases
@enriquep4857 Жыл бұрын
Is it possible to use this if i have protein ID from uniprot instead of genes names?
@asifmolbio Жыл бұрын
Yes it is
@joannagouliou2644 Жыл бұрын
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 Жыл бұрын
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 asifalikalas@foxmail.com
@joannagouliou2644 Жыл бұрын
@@asifmolbio Thank you! I sent them.
@momaz41432 жыл бұрын
and please what is the diference between "STRING" and "Netwrok" in your platfrom? thanks,
@asifmolbio2 жыл бұрын
String is the name software which creates interaction and network is the final form of interactions
@momaz41432 жыл бұрын
@@asifmolbio Many thanks, do you mind please explain how fold enrichment is computed in your pltform, if fold enrichment is relative calulation?
@asifmolbio2 жыл бұрын
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 Жыл бұрын
Hi, will we be able to obtain KEGG pathways just for 8-10 select genes !?
@asifmolbio Жыл бұрын
You can try
@mahjabeenmahjabeen1137 Жыл бұрын
@@asifmolbio I tried but, not able to do so
@asifmolbio Жыл бұрын
Which is your specie mske sure your ID format is ok
@avinafisa47112 жыл бұрын
great!keep it up
@asifmolbio2 жыл бұрын
Thank you, I will
@marwatawfik3956 Жыл бұрын
Thanks. Is it preferable to run each of down and up regulated gene list seperately?
@asifmolbio Жыл бұрын
No need of separate
@marwatawfik3956 Жыл бұрын
@@asifmolbio Thanks again. so the enriched output is considered up regualted or down regulated if my comparisoin is B vs A?
@RahulSk-sp4zy Жыл бұрын
thank you very much, sir, this video is very helpful for me. Sir, do you have a video for a related gene search?
@asifmolbio Жыл бұрын
kzbin.info/www/bejne/gpaxm6ahl6triLs
@MB-vd6hc2 жыл бұрын
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?
@asifmolbio2 жыл бұрын
First select GO category. Go biological functions, cellular component or molecular functions then try
@shandanaaali7498 Жыл бұрын
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 Жыл бұрын
Thanks, Please change your accessions IDs corresponding to NCBI. Sometimes local databases IDs are not indentified by SHINY GO and iDEP.
@husnainahmad4749 Жыл бұрын
can we do gene ontology annotation by using NCBI gene IDs?
@asifmolbio Жыл бұрын
Yes Gene ID not recognized problem: Gene ontology enrichment analysis using GO shiny tool kzbin.info/www/bejne/m5Oze5KagZemqdU
@nurulnadzirah2982 жыл бұрын
sir, what paper do you use in 9.17 mins. Can you provide the link to that paper? TQ
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 Жыл бұрын
Yes you can
@vinitha2774 Жыл бұрын
@@asifmolbio Thank you for your response.
@researcher7410 Жыл бұрын
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 Жыл бұрын
i will upload a video how to solve the problems of id not recongnized. stay tuned
@JourneyGrowthHub2 жыл бұрын
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?
@asifmolbio2 жыл бұрын
It depends what you have already done, and what’s remaining share your complete plan or ppt with me by email: asifalikalas@foxmail.com
@wpzhddd52122 жыл бұрын
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?
@asifmolbio2 жыл бұрын
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
@riteshchandra60732 жыл бұрын
How to download this gene list.
@asifmolbio2 жыл бұрын
*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
@riteshchandra60732 жыл бұрын
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.
@riteshchandra60732 жыл бұрын
@@asifmolbio ok i will check thanks for your support and help.
@asifmolbio2 жыл бұрын
@@riteshchandra6073 please look up in table 2 in the mentioned link
@aviksarkar6138 Жыл бұрын
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 Жыл бұрын
Dear Avik, thanks for message. I will make a new video soon
@aviksarkar6138 Жыл бұрын
@@asifmolbio Thank you Sir...
@deeptirao5982 Жыл бұрын
We are giving only gene names as input, how does it calculate FC, p-value, etc. Please explain.
@asifmolbio Жыл бұрын
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 Жыл бұрын
@@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 Жыл бұрын
@@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.
@DilawarAbbasPhD2 жыл бұрын
Kindly make a Video on how to use statistics 8.1 software
@asifmolbio2 жыл бұрын
Thanks stay tuned , will upload a video about this
@DilawarAbbasPhD2 жыл бұрын
@@asifmolbio thanks 😊
@vijeta9495 Жыл бұрын
After clicking on KEGG it shows diagram downloading can take 3 minutes but not getting the diagram. Please help me out
@asifmolbio Жыл бұрын
Can you change to good internet, i never faced this issue.
@vijeta9495 Жыл бұрын
@@asifmolbio But i m not facing the same problem when doing with demo genes on same system and same internet connection
@asifmolbio Жыл бұрын
Can you send your screenshot of problem and list of genes to me at asifalikalas@foxmail.com
@vijeta9495 Жыл бұрын
@@asifmolbio Please check your mail id
@samvedkulkarni4705 Жыл бұрын
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 Жыл бұрын
You don’t have legend along your main figure to compare gene number ?
@sg40242 жыл бұрын
Great video Sir.Thanks a lot! What to do if we have a list of proteins and want to see protein ontology?Please guide.
@asifmolbio2 жыл бұрын
You can try with proteins ID hopefully it will work
@sg40242 жыл бұрын
@@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.
@swarnadabral2 жыл бұрын
Sir, can you please explain what is fold enrichment?
@asifmolbio2 жыл бұрын
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.
@ayeshawadoodwadood56792 жыл бұрын
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?
@asifmolbio2 жыл бұрын
Try to switch those genes IDs with other databases like ensemble, NCBI or phytozome
@ayeshawadoodwadood56792 жыл бұрын
@@asifmolbio i am using NCBI database. while ensembl plant is not working.
@asifmolbio2 жыл бұрын
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
@ayeshawadoodwadood56792 жыл бұрын
@@asifmolbio Thank you
@chusman71952 жыл бұрын
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
@asifmolbio2 жыл бұрын
kzbin.info/www/bejne/bKSxqoGPfcSpaLc
@asifmolbio2 жыл бұрын
Please see this video it’s related
@chusman71952 жыл бұрын
@@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?
@zohairaqayyum41432 жыл бұрын
Will this tool used to ontology of miRNA as well?
@asifmolbio2 жыл бұрын
yes it can be used for miRNAs gene ontology but you need to use gene IDs rather than name of genes.
@zohairaqayyum41432 жыл бұрын
@@asifmolbio Thank You
@zohairaqayyum41432 жыл бұрын
@@asifmolbio is NCBI accession number accepted here or not?
@asifmolbio2 жыл бұрын
@@zohairaqayyum4143 not accession number of NCBI, but gene ID given in NCBI database can be accepted
@zohairaqayyum41432 жыл бұрын
@@asifmolbio ya right Thank You Sir.
@charmyshah8944 Жыл бұрын
Hi, so can I use this for microarray data that I got for DEG from GEOdatasets?
@asifmolbio Жыл бұрын
Yes you can use
@nusrathfathima3471 Жыл бұрын
Can we paste protein unimportant ID here
@asifmolbio Жыл бұрын
Protein unimportant or protein uniprot ID?
@nusrathfathima3471 Жыл бұрын
@@asifmolbio yes , Uniprot ID of protein profiling data of control and disease
@asifmolbio Жыл бұрын
Technically It should work, you can have a try
@nusrathfathima3471 Жыл бұрын
@@asifmolbio Got results ..but unable to get Kegg and Iam not sure whether the IDs control vs patient is corrector not
@nusrathfathima3471 Жыл бұрын
@@asifmolbio Sir, I drop email we will discuss further their .
@muhammadanees20082 жыл бұрын
My desire specie database is not available , could you please tell us that how can we specie database?
@asifmolbio2 жыл бұрын
Yes some species are not available, you can use it by default search, and no need to select any specie
@muhammadanees20082 жыл бұрын
@@asifmolbio Thank you!
@sanjaisrao4842 жыл бұрын
Thanks
@asifmolbio2 жыл бұрын
Glad you like it
@raminderkaur62632 жыл бұрын
Hi sir, can we use it for Triticum aestivum?
@asifmolbio2 жыл бұрын
Yes can
@trishitabose22285 ай бұрын
Excuseme sir -The site is not at all working the way you did give another webserver
@asifmolbio5 ай бұрын
Are you using vpn
@asifmolbio5 ай бұрын
I have checked Go shiny version 0.80 is working without any vpn
@trishitabose22285 ай бұрын
What is vpn sir?
@trishitabose22285 ай бұрын
@@asifmolbio i tried all versions still i got 0 response, its showing reconnecting like that.
@asifmolbio5 ай бұрын
From which country you are trying to access? Can you change internet i am sure its working
@israr25472 жыл бұрын
ISRARUL HAQUE
@snehaunni1942 жыл бұрын
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
@asifmolbio2 жыл бұрын
Thanks sneha, you can post your questions in-comments here or contact me at asifalikalas@foxmail.com