Interpretation of RNA-seq heat maps

[@nihalahmed1403]

Thanks for keeping it in English. It helps South Indians a lot!

[@asifmolbio]

Yes thats why i choose English. Glad if it’s proving helpful

[@TaranKhan-hl7rn]

Very good work. Thanks

[@asifmolbio]

Glad if you like it

[@JoeL-ry9fq]

Excellent explanation. Well done. 👍

[@asifmolbio]

Glad you like it

[@meemmerani]

thanks so much teaching it in very simple and easier way

[@asifmolbio]

Glad you liked

[@Mr-Ejaz]

Very informative

[@samkhan7536]

thanks for sharing very informative video.

[@asifmolbio]

My pleasure

[@mitrabinda1992]

How many genes should be selected for creating heatmap and how to select the DEGS for heatmap

[@asifmolbio]

Top 15-20

[@mitrabinda1992]

Top 15 to 20 DEGs having larger fold change? Please tell me how to get IDs for GO and KEGG

[@asifmolbio]

@@mitrabinda1992 yes with highest DEGs

[@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

[@mitrabinda1992]

Thank you so much....

[@asktayyabrehman]

Amazing video. Thanks

[@asifmolbio]

Glad you like it

[@dialecticalveganegoist1721]

what do the accolades/brackets on the left side mean?

[@asifmolbio]

Please tell me screen time in video, I will have a look into video

[@dialecticalveganegoist1721]

@@asifmolbio @0:37
The black dendograms on the left side of the figure

[@asifmolbio]

​ Oh, I got it. Actually, a heat map coupled with phylogeny (hierarchical relationships) is called an interactive heat map and that specific network is called a "dataframe". Here each line is representing one gene. The whole network is similar to that of a phylogenetic tree, however here the relationship is decided by gene ontology, not by genetic distance. In other words, the lines having common branches are showing similar types of gene ontology and vice versa.

[@dialecticalveganegoist1721]

@@asifmolbio Thank you professor! 😊

[@avinafisa4711]

👍You always done a great job

[@asifmolbio]

Thanks so much

[@sanjaisrao484]

Thanks

[@asifmolbio]

Welcome

[@tzvi7989]

You should not use FPKM as a normalisation method lmao

[@asifmolbio]

I said, we can use fpkm values to generate heat map in softwares like iDEP. I didn’t use it for normalization

[@tzvi7989]

@@asifmolbio fair play. Guess it doesn't matter so long as it's a normalised unit as you should z-scale it after

[@asifmolbio]

Yes i agree with this point

[@tzvi7989]

@@asifmolbio personally though I'd still use TMM/DESeq2 normalised values, specifically ones that had been rlog/vst transformed

[@asifmolbio]

@@tzvi7989 would you like to make a short tutorial on this ?