Volcano plots explained | How to interpret a volcano plot for DGE

In this video I will explain what is a volcano plot and how to interpret it when representing gene expression data.
Learn what is a volcano plot, how to quickly identify significant genes, and genes that are upregulated and downregulated.
Hope you like it!
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If you liked this video or found it useful, please let me know! Your comments and feedback are very much appreciated😊
If you have questions, don't hesitate to leave me a comment down below, I will answer as soon as I can:)
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More volcano plots resources:
In this video, I explain how to create your own volcano plot in R:
• Volcano plots with ggp...
This is also a really cool tool made with RShiny which allows you to customise your own volcano plot online:
huygens.scienc...
And here is a nice, short explanation on how to interpret volcano plots:
www.htgmolecul...

[@janahanke5420]

this video saved me... my assignment would have been a fail otherwise, thank you so much!!

[@biorainbows4313]

What a great explanation! Thank you so very much :)

[@DarkBumbelsztein]

this video was so clear and so nice!!! thanks so much. PCA plots next, please!! a super lost Metabolomics student here

[@biostatsquid]

Hi Julia thank you very much, this means a lot! PCA plots definitely on the list;)

[@MsFireroll]

Very great ! But 9/3=2 ????

[@domi1096]

I was wondering the same...

[@AyrodsGamgam]

just a typo, she meant 6/2

[@gopalkalwan7465]

6/2 should be there because the purpose was to get 2 fold

[@kiplimosimon1429]

I enjoyed the explanation. it is very clear. Thanks so much

[@nehapimpalwar7339]

VERY INFORMATIVE VIDEO, THANKS A LOT IT MADE MY LIFR EASIER

[@PesPes-t9t]

the first example of gene 1 shows the value for A=3 and B=9 so the FC should be 3 of 2 ?????????? Im not sure but plz respond, i want to have a better understanding of the topic

[@biostatsquid]

Hi, thanks for your comment and sorry for the confusion, it's just a typo! What I meant to have there is expression in A = 3, expression in B = 6 (so twice the expression) -> 6/3 = 2 -> log2(2) = 1. Hope this makes sense now.

[@PesPes-t9t]

thank u @@biostatsquid

[@matheusalmeida773]

Fantastic explanation! Thank you very much!

[@maheshrani6609]

well explained....simple but very effective.

[@nathanieldanielrabo2423]

Exceptional. Thanks 🎉

[@AbhishekVerma-xw3lz]

3:16 The value of gene expression in B should be 6 instead of 9. On a side note, the video provides good explanation.

[@SashaAnronikov]

amazing. thank u biostats squid

[@nidhisingh7066]

you explained this in a very nice way!!

[@biostatsquid]

Thank you Nidhi! Glad it helped:)

[@efrainm4649]

9/3 = 2???? Common dude. You didn't even explain where does the p-value come from...

[@mohamedirfan5480]

Keep making videos ma'am. This is the future of biotechnology. You are a saviour. God bless this channel!!

[@MarkCiuffetelli]

Excellent explanation!

[@folenspill]

Thank you for a very nice video. I have trouble understanding the fold change for gene 1 in the table example. Wouldn't the fold change (FC) be 3 (9 divided by 3) and log2(FC) 1.585?

[@biostatsquid]

Yes, apologies, that was a typo! You are correct:)

[@AzminaAlisa]

Easy and simple to understand! Thank you so much for your comprehensive guidance!

[@alejandrotorres8586]

Excellent explanation. Greetings from Mexico

[@odothomas1851]

Amazing. Thank you

[@nami17]

This was really helpful! Thank you :)

[@asmaal-yousofi3165]

Very useful thanks

[@sumalatha1263]

Useful thanx

[@rabeeakhan563]

please make videos using multiple bioinformatics tools to interpret RNA seq data.

[@biostatsquid]

Thanks for your suggestion! Will definitely do:)

[@lakshmipriyaridevi1033]

Helpful.

[@kibuasmr4423]

Awesome vid, thanks !

[@nasserbenomar]

thank you so much

[@manjinderkaur-hf5pb]

Very useful

[@PerlaAlejandra009]

Always the side right is where are upregulating genes and the downregulated genes are in left side?

[@biostatsquid]

Hi Perla, thanks for your comment, it is a great question. It actually depends on how YOU (or the author of the plot) decide to represent the data, but usually YES, you would like to have upregulated genes (FC > 0) on the right, and downregulated genes (FC < 0) on the left. It's just more intuitive and easier to interpret. But it's all relative. An example. You are comparing DEGs in liver cells versus neural cells. If genes on the right are UPREGULATED in liver cells versus neural cells, then it means they are DOWNREGULATED in neural cells versus liver cells. So it's always important to specify the groups you are comparing and which one is your 'base' or 'control' group. Hope this makes sense!

[@muttugoudr2346]

thank you!

[@debojittalukdar5196]

Extremely Good and helpful video....I need more videos on MA plot, PCA plot, Kegg ,Bubble plot and Heat Map Analysis..Please .

[@dr.tranngocthien]

thank you

[@vinton1881]

Clear explanation! Thank you

[@anujvermabiotech]

Thanks

[@chrisp7336]

Very useful thanks

[@MHiol1]

Thank you.

[@sanjaisrao484]

exellent thanks

[@sanariaaljaf9619]

This was such an informative video! Helped explain so much for me as I have never been exposed to Volcano plots before. Will definitely be tuning in more for more videos! Thank you.

[@JorgeCastillo-ko3im]

Very well explained. Easy to understand. Thank you.

[@biostatsquid]

Thank you! I'm glad it was useful:)

[@daniiujes9577]

What a video

[@martagarcia1946]

Amazing explanation! Thank you very much! Love all your videos, I can understand everything! :)

[@trixstandflipped]

Fantastic video explained in simple yet very applicable terms. Thank you!

[@AyrodsGamgam]

every now and then you find a really nice video that explains something you have a struggle with because the idyot prof in class don't know how to explain it, and so this video is a gem and in a couple minutes does the unthinkable. Thank you Madam.

[@raha1603]

As usual, it is very clearly explained and yet very informative, thanks.

[@MrAseem777]

Precise and clear..great effort.. waiting for such useful videos

[@shabihaheea39]

Very helpful

[@parsaarabshahi6600]

very useful thank you!

[@biostatsquid]

Glad it was helpful!

[@spalding5198]

You don’t know just how happy you’ve made me! Thanks immensely for what you do!!!

[@AmelieHarris-k4j]

That was incredible thank you :)

[@janelu3990]

9/3=2 ？

[@partha_plethorapedia]

very nice explanation...thank you.

[@lucianosouza6766]

it is a well done video. Thank you so much ;)

[@mobeenshaik9164]

keep on doing this beautiful work

[@zahraaalawadly8583]

The video is really so useful. Thank you!

[@lamaismaiel9870]

It is very nice and well-explained, thanks!

[@rayees.ahamed]

Well explained. Thank you.

[@ruthgyereh1052]

More than useful. You’re a star

[@koustavroy350]

Very clear presentation

[@Claireshoon]

That's really clear and thank you: please next OPLS-DA

[@biostatsquid]

Glad you found it useful Shoon! And thanks for your suggestion, I will definitely add it to the list:)