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The GTEx (Genotype-Tissue Expression) Project: Correlations between genotype and tissue-specific gene expression levels will help identify regions of the genome that influence whether and how much a gene is expressed.
Each transcription factor binding site within a cis-regulatory module contributes information about when, where, or how much a gene is turned on, and by dissecting the modules driving a given gene, all the inputs governing expression of the gene can be accurately identified.
However, when, where, what and how much a gene is expressed are regulated precisely and dynamically at multiple levels, including at transcription, mRNA maturation, alternative splicing, and translation levels.
One obstacle is that unlike SAGE, these methods tell you how much a gene is expressed relative to other genes, so it will be hard to compare results across experiments.
The researchers then examined the activity of a gene implicated in flexible behavior, and found that "epigenetic marks" (which determine how much a gene is expressed) were altered in this gene, in the brain and the sperm of the stressed fathers.
The expression value obtained in this step is a measure of how much a gene is expressed in a sample compared to all the other samples in the dataset.
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The discovery of higher-level mechanisms that adjust how much protein a gene makes is a persuasive argument for a more integrated understanding of biology.
Scientists have long suspected that if a retrovirus happens to infect a human sperm cell or egg, which is rare, and if that embryo survives-which is rarer still-the retrovirus could take its place in the blueprint of our species, passed from mother to child, and from one generation to the next, much like a gene for eye color or asthma.
How much does a gene tree differ from the species tree?
All three methods also provide significance scores for final ranks showing how much higher a gene is placed in the inputs than expected.
Sex Bayesian z-scores, in contrast, are specific to each gene; they are a quantitative measurement of how much an individual gene is differentially expressed between sexes (see Methods).
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