excel and most up/down regulated

Question

[candidatusae]

hello everyone, my question is I have a mutant and wild gene analysis in excel. I did t-test and fold change, I have up-regulated bigger than 1.50 and down-regulated smaller than 0.67. my question asked most up and down regulated 10 genes. should I take 1.50 to bigger and 0.67 to smaller genes on my paper? what is a meaning of most up-regulated and most down-regulated genes?

Thank you

[GenoMax]

Is use of excel a requirement for your assignment since that is the last thing you should be using for this analysis.

what is a meaning of most up-regulated and most down-regulated genes?

If you already did the analysis then you must know what that means. If you were asked to provide 10 up and down regulated genes then do the fold change values matter?

[candidatusae]

Thank you I will read...

[ivivek_ngs]

If your data is coming from RNASeq, please ask for the output from the Bioinformatician that performed the analysis and sit with the person to get the most relevant differentially expressed genes based on your biological hypothesis. Get over excel please, not the right thing to use. If you have performed the test then as genomax stated , you should know what your Fold changes are speaking about, coming to your top 10 DEGs, how does really the Fold changes matter in that case?

Answer 1

[Sergey Naumenko]

Dear candidasusae,

Differential expression analysis is one of the most elaborated analyses in bioinformatics, with excellent guidelines and packages available.

I'd suggest reading one of those to improve your analysis, because if you are going to publish the results, you'd like to use reproducible methods rather than 't-test in excel'.

A couple of suggestions to start with:

• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4387895/
• http://bioconductor.org/packages/release/bioc/html/edgeR.html

After reading and applying edgeR or DeSeq2 don't hesitate to ask additional questions.

Good luck! SN

[WouterDeCoster]

I would like to add this RNA-seq workflow from bioconductor to your list.