Hi, I think it will depend on what genes you are looking at and what is the expected expression levels of these genes. If is a low copy number gene, for example a olfaction gene or a GPCR, it expression levels might not change a lot. I saw some publications where they consider FPKM higher than 1. I consider log2fold change >2, FPKM >1, FDR >0.05, and its biological significance as well as the tissue you are analyzing. Sometimes heat-maps can give you a better idea of expression patterns of functional groups of genes over time series data. Luciano

On Wed, Sep 19, 2012 at 5:28 PM, Du, Jianguang jiandu@iupui.edu wrote:

Dear All,

I am comparing the gene expression between two cell types by examining the Cufflink output file -- gene differential expression testing. The file lists the FPKM of genes in two cell types and log2 of fold. I want to look for genes that have more than 2-flod of expression in cell type A than in cell type B. What is the minimum FPKM in cell type A so that only the genes that have FPKM highier than this number can be taken into consideration for further analysis?

For example,

The FPKM of gene X in cell type A is 80, and in cell type B is 20, the fold of difference is 4.

The FPKM of gene Y in cell type A is 4, and in cell type B is 1, the fold of difference is also 4.

Is there a minimum FPKM in cell type A for genes to be selected for further analysis?

Thanks.

Jianguang

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