Question: up regulated and down regulated genes in co expression network
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gravatar for izsyed16
18 months ago by
izsyed1610
izsyed1610 wrote:

Hi all, I am making a co expression network using gene micro array data via Pearson correlation. If I consider a threshold value of 0.95 for correlation coefficient then my question is that should I consider positive correlation coefficient or both (positive and negative correlation values) for making network.

ADD COMMENTlink modified 18 months ago • written 18 months ago by izsyed1610
1
gravatar for Jean-Karim Heriche
18 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

Consider what the correlation means. A positive one means the genes vary linearly in the same direction, i.e. they are both up or down-regulated whereas a negative one means the genes vary linearly in opposite direction, i.e. when one is up-regulated the other is down-regulated and vice versa. Now, ask yourself what is relevant to your biological question.

ADD COMMENTlink written 18 months ago by Jean-Karim Heriche18k
0
gravatar for munizmom
18 months ago by
munizmom60
munizmom60 wrote:

Depends on which question you are interested on answering. If you are interested in identifying only the genes that are positive correlated or negative correlated or both...are you interested in identifying genes whose expression is upregulated or down regulated but follows the same direction (positive correlation) or are you interested in identifying genew that are negative correlated so in one condition are up regulated and in another downregulated?

ADD COMMENTlink written 18 months ago by munizmom60
0
gravatar for izsyed16
18 months ago by
izsyed1610
izsyed1610 wrote:

Can I consider both scenarios simultaneously that is can I take positive correlation (up regulated and down regulated simultaneously) and negative correlation (up regulated versus down regulated inversely) in one network that is can I take threshold as follows, correlation>0.9 and correlation <-0.9(more negative). Is it logically correct?? and what is biological relevance of such gene co expression network. If network is Un-directed?

ADD COMMENTlink written 18 months ago by izsyed1610

You can use the absolute value of the correlation. This is an 'unsigned' network. Logically it is correct but the interpretation changes as others have pointed out.
You can read more here: http://www.peterlangfelder.com/signed-or-unsigned-which-network-type-is-preferable/

ADD REPLYlink written 18 months ago by Jake Warner690
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