How to perform Weighted gene co-expression network analysis (WGCNA) without coding?

[@Nature520-k6i]

This is really amazing and easy explanation. I will do this type of analysis in near future. and refer to your video

[@asifmolbio]

Glad if it’s helping

[@samkhan7536]

Very informative lecture

[@asifmolbio]

Glad you like it

[@sreeram6416]

sir tutorial nicely explained but please explain the theory bit more in detail

[@asifmolbio]

@@sreeram6416 this analysis is about performing WGCNA analysis

[@asifmolbio]

@@sreeram6416 for interpretation i will record separate

[@prashanthjavali4182]

Hi sir this is very usefull video , My question is if i have microarray data specially expression profiling by array and i want to perform WGNCA analysis can i able to performe with idep server ? If yes kindly help me on this

[@asifmolbio]

Yes, you can

[@prashanthjavali4182]

@@asifmolbio sir how to do that sir can u please explain me

[@asifmolbio]

upload your expression file in excel similar to i have done in this video

[@prashanthjavali4182]

@@asifmolbio only expression file is enough ???? no need of design file??

[@asifmolbio]

let me send you a design file video

[@tanusreedatta4493]

Hello brother, is it only for Arabidopsis or I can use other plant ids?

[@asifmolbio]

Any specie is okay

[@tanusreedatta4493]

@asifmolbio Okay Thank you. Here you have mentioned that, it is applicable for 15 samples. Samples means control and treatment plant numbers? Or something else! Cause I have one control and 2 treatments. Can I do WGCNA with these?

[@asifmolbio]

@@tanusreedatta4493 total including control, treatment and replicates should be more than 15

[@tanusreedatta4493]

@asifmolbio Okay got it. Your videos are too helpful brother. I watch your videos and the explanation is better than other videos. I am in Zhengzhou University, Henan, China, doing PhD with Agriculture field. Could you please share your wechat?

[@tanusreedatta4493]

@asifmolbio Thank you brother

[@taramin873]

one more question 🙋 which step can I set the p.value to 0.05? THANK YOU^^

[@asifmolbio]

In the iDEP tool

[@asifmolbio]

In the start of analysis

[@Paachi8651]

Sir,where s ur institute, want to come and learn especially R,python,WGCNA, Deseq2,Roc, PCA .Practical ly i want to learn ,m doing phd in bioinformatics without nothing,Can u pls help me .

[@asifmolbio]

I am based in china at present. One to one session can be booked: if needed go to about section on KZbin channel and fill the form

[@Paachi8651]

Where will I get the link and fill the form ji

[@asifmolbio]

www.youtube.com/@asifmolbio/about

[@mdsymunrabby7625]

How do I get the Design file of the specific gene ID?

[@asifmolbio]

Need to create by yourself see the video on my channel to learn

[@taramin873]

Thanks for sharing this video you kinda saved me I still have question, what is the edge threshold thank you^^^^^^^

[@asifmolbio]

Welcome you can start by setting it to 0.5 as a starting point.

[@sakibsarkerii514]

Sir, I have been following your videos from last one year. I have learned a lot of things from your videos. Sir, can u make a video about how to apply WGCNA in microarray dataset using R? Please sir, I will be very grateful if you make a video on this topic. I have been trying to perform WGCNA in GSE62232 but I am failing.

[@asifmolbio]

Thank Sakib, Sure i have noted down your topic, i will make a video soon inshaAlllah.

[@sakibsarkerii514]

@@asifmolbio Thank you so much sir.

[@sakibsarkerii514]

​@@asifmolbio sir can we expect the video near future? Plz sir

[@RjAtifAyub]

If sample size is less then 15 then what we should do?

[@asifmolbio]

Then authentication of wgcna can be questionable to some extent.

[@sanjuktaghosh8802]

Hi Dr Asif. You said atleast 15 samples. So, is it total 15 samples taking all groups or each group should have 15 samples? Also do you have a video where you have prepared the gene count file from RNA-Seq sample data?

[@asifmolbio]

All the samples from all groups should be more than 15, not from one group

[@asifmolbio]

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

[@sreeram6416]

design file is the metadata file know sir

[@asifmolbio]

Design file is for choosing treatments comparisons

[@nikhilchand5329]

I am performing iDEP with gene ids of wheat. But on loading data in iDEP it shows disconnected from the server. Please provide any suggestion to resolve the problem.

[@asifmolbio]

I never faced any problem like this. Probably website will be under maintenance you can try after a day or two.

[@nikhilchand5329]

@@asifmolbio Okk sir Any alternative to do WGCNA

[@asifmolbio]

Alternative is through R programming. But i am sure, website will be functional. You can try after changing internet or computer

[@nikhilchand5329]

@@asifmolbio okk sir

[@kumaka6]

check your input data whether it is in correct format. may i know how many samples you have given as input.

[@nikhilchand5329]

Good afternoon sir I am using list of wheat gene ids with TraesCS4D02G203800 but iDEP showing error I'd not recognised. What I have to do sir?

[@asifmolbio]

Can you change the gene and try any other id ? Still same

[@subhankarraha4033]

Dear sir, i want to verify some genes of my interest are co-expressed or not via this iDEP tool. Is it possible, is their any need of special R coding If I want to check specific genes are responsible for specific hormonal pathway. can I do it via this iDEP tool? ( If the RNA SEQ data is not available in iDEV itself) Thank you in advanced

[@asifmolbio]

There is no tool to verify to find genes co expressing. You need to look your pathway by yourself from all pathways Watch this video to get an idea

[@asifmolbio]

How to select genes for qPCR validation in transcriptome/RNA seq data? kzbin.info/www/bejne/hoPLeXWZn7B0gbc