7.1 years ago by
The gene expression ratio results of a cuffdiff analysis are found in the file: gene_exp.diff. Each row of the file represents a gene measured under two conditions. There are three essential columns you need to answer your question: value_1, value_2, log2(fold_change). The value_1 column contains FPKM values for each gene in sample 1. The value_2 column contains FPKM values for each gene in sample 2. The log2(fold_change) column represents the ratio of the two measurements as: log2(sample_2/sample_1). Since it is in log2 space, positive values mean enrichment in sample_2 over sample_1, and negative values mean enrichment in sample_1 over sample_2. As pointed out by Sam, because it's easy to have 0 reads for some genes in either sample, you will get +Inf and -Inf when taking a ratio that has 0 in either the numerator or denominator. Thus the answer to your question is that in your list, the genes with positive values in the log2(fold_change) are enriched in sample_2 (what you are referring to as up-regulated), and those with negative values are enriched in sample_1 relative to sample_2 (which you refer to as down-regulated). Keep in mind however, that enrichment is an observation, up or down-regulation is a mechanism. You are observing enrichment, not a mechanism.