Upregulated And Downregulated Genes

Question

[Varun Gupta]

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

[Manu Prestat]

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

[Varun Gupta]

Well data is rna seq so yes transcripts my mistake

[Arun]

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.

Answer 1

[Damian Kao]

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.

[Ryan Dale]

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

Answer 2

[ff.cc.cc]

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