Question: up regulated and down regulated genes in co expression network
0
gravatar for izsyed16
3.0 years 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 3.0 years ago • written 3.0 years ago by izsyed1610
1
gravatar for Jean-Karim Heriche
3.0 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche23k 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 3.0 years ago by Jean-Karim Heriche23k
0
gravatar for munizmom
3.0 years 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 3.0 years ago by munizmom60

".are you interested in identifying genes whose expression is upregulated or down regulated but follows the same direction (positive correlation)" Would it be logical construct a co-expression network of only upreg or downreg genes instead of accommodating genes of both types?

ADD REPLYlink written 9 months ago by Arindam Ghosh310
0
gravatar for izsyed16
3.0 years 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 3.0 years ago by izsyed1610
1

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 3.0 years ago by Jake Warner810
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 910 users visited in the last hour