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Functional analysis of microarray gene lists


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4 replies to this topic

#1 Tabaluga

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Posted 27 September 2013 - 01:20 PM

Hi,
let's say I have a gene list, derived from a microarray, and have determined by a David database search that most of the genes are involved in cell cycle regulation/proliferation/mitosis. How can I find out whether they are positive or negative regulators of the cell cycle ? Do I have to look up every single gene or is there also a way to determine this for a whole list of genes ?

Il dort. Quoique le sort fût pour lui bien étrange,
Il vivait. Il mourut quand il n'eut plus son ange;
La chose simplement d'elle-même arriva,
Comme la nuit se fait lorsque le jour s'en va.

 


#2 theo22

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Posted 28 September 2013 - 02:30 AM

I suppose that you obtained the mRNA for this microarray from cells that were treated or untreated with something? Then I would take the same cells, treat them the same and measure cell-cycle progression by PI-staining or BrdU incorporation.

 

If you obtained your sample from living animals, you can still do the BrdU incorporation and look at incorporated BrdU by histology.

 

If you would like to get a more specific answer, you will need to be more specific about the experiment you performed.


Edited by theo22, 28 September 2013 - 02:31 AM.


#3 Tabaluga

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Posted 28 September 2013 - 11:27 AM

Thanks for the reply, but I'm actually not looking at all for an experimental way to determine proliferation. I just wanted to ask if there is a way to determine at the computer screen, bioinformatically, if the genes are positive or negative regulators of proliferation. If there is no other possibility I will have to look up every single gene then, but as this takes a lot of time I was hoping that there is an easier way.

Il dort. Quoique le sort fût pour lui bien étrange,
Il vivait. Il mourut quand il n'eut plus son ange;
La chose simplement d'elle-même arriva,
Comme la nuit se fait lorsque le jour s'en va.

 


#4 Mikhail Shugay

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Posted 03 October 2013 - 06:48 AM

Thanks for the reply, but I'm actually not looking at all for an experimental way to determine proliferation. I just wanted to ask if there is a way to determine at the computer screen, bioinformatically, if the genes are positive or negative regulators of proliferation. If there is no other possibility I will have to look up every single gene then, but as this takes a lot of time I was hoping that there is an easier way.

In theory GO is detailed enough to distinguish positive and negative regulation of cell proliferation (http://www.ebi.ac.uk...m?id=GO:0008284)

So if you'll get the corresponding GO categories and check abundance of genes annotated with them you could perhaps answer your question.



#5 Tabaluga

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Posted 07 October 2013 - 04:40 PM

Thanks, I'll still have to check the single genes then as it seems (or am I missing something ?) but I will try now !


Edited by Tabaluga, 07 October 2013 - 04:40 PM.

Il dort. Quoique le sort fût pour lui bien étrange,
Il vivait. Il mourut quand il n'eut plus son ange;
La chose simplement d'elle-même arriva,
Comme la nuit se fait lorsque le jour s'en va.

 





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