how to find the gene expression of a given gene in human genome

Question

[Mo]

Hi,

I want to be able to identfify the expression level of CDKN1A in human genome.

Here is my thought, this gene repeats at 6p21.2 so how can I get the expression or what steps do you think I should take to be able to quantify this from human genome?

Answer 1

[Jeremy]

You can use qRT-PCR or targeted RNA-Seq.

[Mo]

Any other way to check from whole human genome?

[Friederike]

If I gave you a copy of the Bible and asked you "How many times has the Bible been read? And how many times has each person read the Bible?" -- Would you be able to answer that just by looking at the text of the Bible?

The genome is a (more or less) inert sequence of A, C, T, Gs -- it's the instruction manual, the blueprint, the "text". How that text is being used to make proteins etc., i.e. how the sequence is being expressed is a whole different story and involves RNA. Plus it's a very different story depending on what types of cells at what time of an organisms life span you're looking into it.

The Human Protein Cell Atlas is a better resource to understand how the CDKNA1 locus is expressed in various tissues.

Answer 2

[Michael]

This question really invites us to explain that it is not that simple and that it should not be asked in this way, even though this might seem a little picky at first. Firstly, I would say that genes are not "expressed in a genome". Then, it is important to define if you are looking at RNA/mRNA levels or protein quantification. RNA and proteins are expressed in cells, of which many different types exist in different tissues, and each of the ~37 trillion cells in the human body has its very own expression profile depending on complex regulatory cascades. Therefore, there does not exist a way to infer the expression of a gene from the sequence alone, but it can be measured and also predicted for a specific cell type and splice isoform based on other measurements of, e.g. chromatin accessibility, histone modification, methylation, transcription factor binding, ribosome binding, etc. (see e.g. The ENCODE Project consortium, 2012, and there especially Figure 2).

To better understand the complexity of the task at hand, it is good to take a first look at databases such Human Protein Atlas already mentioned by Friederike or the UCSC genome browser, or maybe the Cancer Genome Atlas. Browse through these resources, and look at different summaries of expression in the genome browser, e.g. opening tracks under the headers "Expression" and "Regulation". Look at the Single Cell Atlas as an entry to more modern single cell sequencing data. This will still give you only a tiny fraction of data about expression of Cyclin dependent kinase inhibitor 1A, but these resources all do an excellent job in summarizing the complex measurements into digestable pieces of information for their users. After that you will be able to state what you are looking for in a more specific way.