How to find genes of interest in RNA-seq / transcriptomic data ? Kegg pathway

[@TajwarSultana-d1o]

Your videos are very significants for the students who don't know anything about MB. APPRECIATED

[@asifmolbio]

Glad if its helpful

[@reynaguillenenriquez6186]

Just in time I needed to know more about this topic.

[@asifmolbio]

Glad its in time

[@poonams4029]

@Dr Asif sir
If we have mean fold change data of treated and untreated group in single excel then how to upload and generate graph from this

[@asifmolbio]

Then its not possible first have to choose data

[@RjAtifAyub]

@Dr Asif your video is informative but this website has limited species so how we can search our data in it?

[@asifmolbio]

Unfortunately, this website is for limited species. You can try bioinformatics.com.cn/en

[@samkhan7536]

brothr tell me about the gene of interest related to various plants hormone like auxin, IAA, Cytokinins , GA

[@asifmolbio]

You can search with one by one keywords after uploading to Divenn

[@Fayezazuuha]

what is recommended software for tomato?

[@Shazi5886]

great but this website has limited species so how we can search our data??

[@asifmolbio]

This website is species limited

[@asitrayinsane]

Can you make a video on wcgna analysis using idep since many of analysis like tom heatmap, adjacency heatmap are missing in idep

[@asifmolbio]

Its already uploaded let me share with you the link

[@asifmolbio]

th-cam.com/video/_zXbgLlObiQ/w-d-xo.htmlsi=ihK1Andqrq6mPY5b

[@yousufshafiq3823]

AOA bhai.... agr hum brassica ka krna RNA seq data analysis krna chahiay to ais site p. Brassica family ka option hi nh

[@asifmolbio]

Wslam right its only limited to a few species only

[@habibalamgamaryani6977]

Very nice, to the point 👍👍

[@asifmolbio]

Glad you enjoyed

[@khanrahatullah6298]

Sir ! How many graph and which graph we can include in our thesis data from transcriptome, please reply me

[@asifmolbio]

Already responded you in email

[@SonuKashyap-gb7vo]

So when you are selecting the p0.05 is it pvalue or adjusted pvalue? Thanks

[@asifmolbio]

Adjusted

[@diyanazulkifli7567]

Sir, is expression value similar as fpkm?

[@asifmolbio]

Yes fpkm is also expression

[@Premkumar-ko3ct]

Sir i have transcriptomic data set in rice regarding nematode infection, resistant and suceptible parent infected vs un infected but i unable to choose which pathways i need to take to write a paper

[@asifmolbio]

How to calculate FC, log2FC, Pvalue, Padj, Up/down genes in RNA seq data using Excel
th-cam.com/video/HH3Mll4W5WE/w-d-xo.html
How to find genes of interest in RNA-seq / transcriptomic data ? Kegg pathway
th-cam.com/video/LeNjskbF8RY/w-d-xo.html
Interpretation of Principal component analysis (PCA) in RNA seq
th-cam.com/video/aUOV7EBGOy8/w-d-xo.html
How to select genes for qPCR validation in transcriptome/RNA seq data?
th-cam.com/video/PRhHBcjKAKU/w-d-xo.html
How to interpret the results of KEGG pathway analysis?
th-cam.com/video/meTGfLVBiRs/w-d-xo.html
How to write and interpret gene ontology (GO) in research articles ?
th-cam.com/video/kRt2IWfhCqU/w-d-xo.html
Interpretation of RNA-seq heat maps
th-cam.com/video/cRT5mpGMDmQ/w-d-xo.html
Interpretation of RNA seq data | DEGs | GO | KEGG
th-cam.com/video/xc2zEI_5pmw/w-d-xo.html
You can watch them in reverse order, last one first and watch one by one while moving up. Hope you will get answers.

[@asifmolbio]

Watch them hopefully, you will select pathway

[@jalilahmad9923]

Thank you Sir

[@asifmolbio]

You are welcome

[@Hotchanna]

I am looking for gene targets of differentially expressed microRNAs. I have been using Transcriptome Analysis Console, but it is very limited in terms of data visualization, thus I have been looking for a free online substitution. Unfortunately, most of what I have tried online do not recognize my samples' accession numbers (MIMAT... and MI...), thus I am unable to use these tools. Do you know of any that would accept my accession numbers? My data contains ~3500 microRNA entries. If this helps: data is from microarray and I do not know how to use R. Thanks!

[@asifmolbio]

Hi kay, you can try uploading those ids with expressions ( of 20 or 10 microRNAs only in first instance) and check if its working.

[@Hotchanna]

@@asifmolbio I will try! Thanks!

[@Hotchanna]

@@asifmolbio Hello! The software successfully accepted the 20 accession numbers, so I tried pasting all of my data. However, your software is telling me I have 1 accession number assigned to more than one miRNA. Which is fine. But considering I have thousands of entries, I will have to delete the replicates one at a time.

[@lifeislife715]

Very nice ®

[@asifmolbio]

Glad you like it

[@susmitasworld4354]

How can we plot when we have only two groups?

[@asifmolbio]

Take one as control and have a comparison

[@faisalaziz8411]

Sir give lecture on the single cell RNA seq analysis tutorial. Thanks

[@asifmolbio]

Yes much needed topic sure thanks for suggestion

[@qixuanhe500]

Nice Video! Does it also apply to proteomics data?

[@asifmolbio]

Yes most of them equally applicable in proteomics

[@asifmolbio]

Yes most of them equally applicable in proteomics

[@qixuanhe500]

@@asifmolbio Thank u！And I have another question: What do you mean by"three treaments" in 3:06? That is, how to process data in three ways?

[@kamalthakur7418]

Thanku sir

[@asifmolbio]

Glad you like it

[@ahmadjutt9718]

hello sir, Can I contact you by WhatsApp or email ?

[@asifmolbio]

[e-mail]

[@ahmadjutt9718]

dear sir, I have sent you an email@@asifmolbio

[@hamzajamil3905]

Thank u very much sir g
can I have your LinkedIn or email?
Just want to ask and know more about thses Transcriptomic tools
I will be very thankful

[@asifmolbio]

Thanks, please do an email to [e-mail]