This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Upregulated And Downregulated Genes

Hi Everyone

Suppose i have a list of all the genes for a particular organism with their read counts under different conditions . Some thing like this

gene_name    condition1    condition2    condition3
geneA    24    48    102
geneB    30    87    147
geneC 128    23    44

and so on..

What i want to know is which genes are up regulated and which of them are down regulated genome wide.

Is there a way to do this.

Let me know

Regards

differential expression
• 8,014 views • link
updated by ff.cc.cc ff.cc.cc • written by Varun Gupta Varun Gupta

I guess it's transcripts, but could you clarify?

• 113 views • link
written by Manu Prestat Manu Prestat

Well data is rna seq so yes transcripts my mistake

• 0 views • link
written by Varun Gupta Varun Gupta

You can not know the "true" expression of the transcripts even though it's RNA-seq (at least not yet to my knowledge). What you've is the number of reads that map to the gene (either including or excluding introns). But it is not transcript expression. That's why it's called differential gene expression.

• 0 views • link
written by Arun Arun

2 answers

You can use any of the popular differential expression R packages. DESeq and edgeR are probably the 2 packages people use most.

DESeq2: http://www.bioconductor.org/packages/devel/bioc/html/DESeq2.html

EdgeR: http://www.bioconductor.org/packages/2.11/bioc/html/edgeR.html

They both have pretty good documentation with multiple examples on how to use the package and interpret the results.

• 115 views • link
written by Damian Kao Damian Kao

Hmm, didn't realize DESeq went 2.0 (dev version at least), thanks for the heads up.

• 0 views • link
written by Ryan Dale Ryan Dale

HI,

Limma (link to bioconductor) is widely adopted for the analysis of gene expression.

Now its documentation (chap. 16 here) include a chapter that deals with the case of rna-seq data

• 107 views • link
written by ff.cc.cc ff.cc.cc

Log in to answer this question.

More posts like this