Right BEL statements

[Afroza Irin]

Hello,
Could you please help me ,how can I represent following statements into BEL script-

1. "Induction of CYP2E1 generated ROS"
2. "Inhibition of DNA methylation activated SNCA expression"

So far I understand here in both cases I have only relation and object term. If subject is not available how to express that?

Thanks in advance .
Bests,
Afroza Irin

[Natalie Catlett]

Hi Afroza,

 

I am making a few guesses based on limited information, but this should give you a general idea.

 

1.       p(HGNC:CYP2E1) -> a(CHEBI:”reactive oxygen species”)

2.       bp(GOBP:”DNA methylation”) -| r(HGNC:SNCA)

 

In case #1, CYP2E1 induction leads to the production of ROS, so CYP2E1 is the subject, increases is the relationship, and ROS is the object.

In case #2, the biological process DNA methylation is the subject and SNCA the object. Because inhibition of the subject leads to an increase in the object, the relationship is flipped to decreases.

 

Best,

Natalie

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[Natalie Catlett]

Hi Afroza,

 

Unfortunately, BEL does not currently handle representation of methylated regions of DNA. This is something we hope to address in a future language update. Until that time, you may consider representing the downstream effects of hypomethylation (e.g., changes in RNA expression). Note that in your example, this would likely be a correlation (rather than a causal increase/decrease) between the disease and the effect of CYP2E1 hypomethylation.

 

Best,

Natalie

 

 

 

From: openbel...@googlegroups.com [mailto:openbel...@googlegroups.com] On Behalf Of Afroza Irin
Sent: Wednesday, April 22, 2015 4:25 AM
To: openbel...@googlegroups.com
Subject: Re: Right BEL statements

 

Hello Natalie,
Thank you so much .It was really helpful. But there are also some other case where its really confusing to understand the function. For example -

  " In PD patient CYP2E1 gene was hypomethylated "

 How could this 'hypomethylated ' term be defined?

 

Bests,
Afroza Irin

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