I am trying to build a gene regulation network, and I need some basic knowledge of it.

So, in gene research, we perturb genes. Such as knock down them?

Can people tell 2 or 3 experiment methods to perturb genes? And 3 or more observations (phenotypes) after perturbation?

If it could be explained in the context of Microarray, it will be well appreciated.

The question is not that organised, if you can tell a whole story before the computational work started, I will thank you so much.

  • $\begingroup$ I'm afraid this is really a bit too broad. Perturbation can mean very many things from changing the expression level, to switching genes on or off, to altering the protein produced. The phenotypes will depend both on the particular perturbation applied and on the specific gene perturbed. $\endgroup$ – terdon May 13 '14 at 15:03
  • $\begingroup$ @terdon Thanks for your comments, What I am asking is how to perturb genes ? How to do experiments to perturb genes ? and what are the possible phenotypes/outcomes after perturbing ? $\endgroup$ – GeekCat May 13 '14 at 19:10
  • $\begingroup$ I'm not sure how you can explain it by microarray, since a microarray only gives a readout at a transcript level, and genetic purturbations can be applied down-stream at a protein level (say by expressing a mutant protein). Also, perturbation studies in vitro are quite diverse as terdon already mentioned. I would suggest reading literature for the types of questions you wish to answer, and see how they were addressed experimentally to better focus your question. $\endgroup$ – user560 May 13 '14 at 19:50
  • $\begingroup$ This questions doesn't fit the SE format too well. While there are several ideas that could be good questions on their own ("how can genes be perturbed?", "what phenotypes result from gene perturbation?", "how is gene perturbation used for microarrays?"), it seems like this question wants someone to write a report tailored to this person's research needs (how many future visitors will benefit from such an answer?). $\endgroup$ – Superbest May 17 '14 at 9:54
  • $\begingroup$ @GeekCat, currently your question is too broad and actually includes several sub-questions. You are more likely to get a good answer if you break it down into distinct separate questions. For a start, I would recommend that you ask "What does gene perturbation mean in the context of gene regulatory networks and how is it achieved practically?" as this will help you to understand what else you need to ask. $\endgroup$ – Armatus May 17 '14 at 11:22

Here are 3:

1) gene knockout. Just delete the gene from the genome. The function is gone - useful for demonstrating a direct involvement of the gene in the phenotype. As a phenotype, the microarray will register all sorts of reactions to the loss of the gene in addition to the RNA in question being gone.

2) use selection to find mutants for the gene. Expose the organism to a mutagen or high amounts of UV radiation. Useful mutants vary by what the function of the genes are. Temperature sensitivity - the gene doesn't function above 30 deg C is an example of a phenotype for a mutant that has been used classically. In this case the functioning of the gene itself is a phenotype. This is an example of a weaker perturbation. Can be used when knockouts are fatal or when the system is too sensitive for a knockout.

3) change the environmental conditions. increase the concentration of a substrate or lower the availability of nutrients. Phenotypes can be rate of growth/division, production of a given metabolite from the cells, but it goes on and on.

The affect on whole genome microarray data can be quite complex in such perturbation experiments because the coupling of many genes, even in bacteria can be broad and significant.

  • $\begingroup$ Thanks, @shigeta, could you please give 3 possible phenotype outcome of it ? $\endgroup$ – GeekCat May 14 '14 at 20:14
  • $\begingroup$ well the microarray itself is often the phenotype itself - RNA production. That's why its so popular as a technique. Mutant studies have a measurable phenotype such as a the amounts of a chemical that is produced in the cell, or the rate of growth. Phenotypes are a very broad topic - they are essentially ANY observable w.r.t. a cell or an organism. that's a very large list if you include observations by instrumentation. Its akin to asking a mathematician to list all the properties of numbers. $\endgroup$ – shigeta May 14 '14 at 20:52

Perturbation is when you either introduce a gene or gene product or inhibit it using a variety of approaches to see what other genes show changes in expression or other epigenetic modifications, which can be measured using a microarray.

If genes A,B,C,D,E are expressed more due to the activity of Gene X while F,G,H are unaffected, when you compare microarray data from samples where X has been turned off to those where it hasn't, you will see decreased expression of A,B,C,D and E - you can represent this as a graph with Gene X being the hub.

Hope this helps, Ankur.


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