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Interpretation of RNA-seq heat maps 

Dr. Asif's Mol. Biology
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21 авг 2024

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Комментарии : 37   
@nihalahmed1403
@nihalahmed1403 Год назад
Thanks for keeping it in English. It helps South Indians a lot!
@asifmolbio
@asifmolbio Год назад
Yes thats why i choose English. Glad if it’s proving helpful
@TaranKhan-hl7rn
@TaranKhan-hl7rn 5 дней назад
Very good work. Thanks
@asifmolbio
@asifmolbio 4 дня назад
Glad if you like it
@JoeL-ry9fq
@JoeL-ry9fq 9 месяцев назад
Excellent explanation. Well done. 👍
@asifmolbio
@asifmolbio 9 месяцев назад
Glad you like it
@Mr-Ejaz
@Mr-Ejaz 4 месяца назад
Very informative
@samkhan7536
@samkhan7536 2 года назад
thanks for sharing very informative video.
@asifmolbio
@asifmolbio 2 года назад
My pleasure
@meemmerani
@meemmerani 2 года назад
thanks so much teaching it in very simple and easier way
@asifmolbio
@asifmolbio 2 года назад
Glad you liked
@asktayyabrehman
@asktayyabrehman 2 года назад
Amazing video. Thanks
@asifmolbio
@asifmolbio 2 года назад
Glad you like it
@avinafisa4711
@avinafisa4711 2 года назад
👍You always done a great job
@asifmolbio
@asifmolbio 2 года назад
Thanks so much
@mitrabinda1992
@mitrabinda1992 3 месяца назад
How many genes should be selected for creating heatmap and how to select the DEGS for heatmap
@asifmolbio
@asifmolbio 3 месяца назад
Top 15-20
@mitrabinda1992
@mitrabinda1992 3 месяца назад
Top 15 to 20 DEGs having larger fold change? Please tell me how to get IDs for GO and KEGG
@asifmolbio
@asifmolbio 3 месяца назад
@@mitrabinda1992 yes with highest DEGs
@asifmolbio
@asifmolbio 3 месяца назад
How to calculate FC, log2FC, Pvalue, Padj, Up/down genes in RNA seq data using Excel ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-HH3Mll4W5WE.html
@mitrabinda1992
@mitrabinda1992 3 месяца назад
Thank you so much....
@sanjaisrao484
@sanjaisrao484 Год назад
Thanks
@asifmolbio
@asifmolbio Год назад
Welcome
@dialecticalveganegoist1721
@dialecticalveganegoist1721 Год назад
what do the accolades/brackets on the left side mean?
@asifmolbio
@asifmolbio Год назад
Please tell me screen time in video, I will have a look into video
@dialecticalveganegoist1721
@dialecticalveganegoist1721 Год назад
@@asifmolbio @0:37 The black dendograms on the left side of the figure
@asifmolbio
@asifmolbio Год назад
​ 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
@dialecticalveganegoist1721 Год назад
@@asifmolbio Thank you professor! 😊
@tzvi7989
@tzvi7989 Год назад
You should not use FPKM as a normalisation method lmao
@asifmolbio
@asifmolbio Год назад
I said, we can use fpkm values to generate heat map in softwares like iDEP. I didn’t use it for normalization
@tzvi7989
@tzvi7989 Год назад
@@asifmolbio fair play. Guess it doesn't matter so long as it's a normalised unit as you should z-scale it after
@asifmolbio
@asifmolbio Год назад
Yes i agree with this point
@tzvi7989
@tzvi7989 Год назад
@@asifmolbio personally though I'd still use TMM/DESeq2 normalised values, specifically ones that had been rlog/vst transformed
@asifmolbio
@asifmolbio Год назад
@@tzvi7989 would you like to make a short tutorial on this ?
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