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I am a PhD student in mathematics, and I will be involved on a project that aims to cluster (i.e. automatically group) people according to their gene expressions.

Well, the project looks very nice, but I have no idea of what gene expressions are and consequently how to model them mathematically. So here are my questions.

Is there a "Gene expression for dummies" manual that I can read, considering that my last studies of biology move back to the high school (10+ years ago)? Any suggestion, also divulgative books?

Is there a good reference to study how gene expressions are modeled under the mathematical point of view?

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I suppose you first need to learn the basics of genetics before investigating the stats behind gene expression clustering. I will based my recommendations on Khan Academy, that is generally speaking a good very introductory source of information for biology and other fields.

Basics of genetics

Here are a few questions for you:

  • What exactly do we call the genetic code?
  • Are you aware that genes are transcribed into mRNA that are translated into proteins?
  • What is an allele?
  • Do you know what is an exon and an intron?
  • Do you know what is a TATA box?

If you answered no to any of these question I would recommend that you have a look at Khan Academy > Central Dogma.

Gene regulation

Then, you should have a look at Khan Academy > Gene regulation

Other

Don't hesitate to have a look at other sections in the biology series of khan academy if you want to broaden your understanding of e.g. what DNA looks like, what is happening at reproduction, how do genes segregate, or other things such as evolution. Typically, Khan Academy > biotechnology could also be helpful as to give you a rough feeling of the methods used to investigate gene expression

Gene expression clustering

The literature on clustering gene expression is very rich (see google scholar).

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You start with the central dogma. This is the idea that information flows from DNA replication to DNA transcription and ends up in DNA translation. These are the three parts of the central dogma. The dogma suggests that DNA is the alpha and translation is the omega. There are many things in-between such as gene splicing and post-transcriptional modification. Also look at the different RNAs (small and large), because genes only lead to protein synthesis, but there are other RNA products that arise from transcription. Anorganic ions also help to synthesize proteins. They come from outside the cell and are not encoded for in DNA. That is epigenetics.

Gene clusters are genes that work together towards a common cause. That cause might be the synthesis of a protein that has a function that serves the cell. Biochemically there are many factors that contribute to a protein's synthesis and genes are some of them.

I think a math person might be interested to know that there are software packages that look for gene clusters. Here's a video:

https://www.youtube.com/watch?v=a3uiIp4gUso

There is no genes for dummies. You can build your house out of straw, wood, or stone. Here's the stone:

https://www.amazon.com/Genomes-3-T-Brown/dp/0815341385

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  • $\begingroup$ As a mathematician who moved into biology I very much agree with your suggestion of genomes 3. Perhaps I got lucky but I managed to get one of eBay much cheaper than amazon. $\endgroup$ – HBeel Sep 25 '16 at 19:12
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I have a copy of this book,The Mathematics of Genome Analysis, it might be right up your alley (even if it is slightly dated).

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