Knockdown experiments

8 views
Skip to first unread message

Anna Procopio

unread,
Jun 6, 2023, 4:54:39 AMJun 6
to cobra-...@googlegroups.com
Hi everyone, 
I have a question. Is it possible to perform knockdown experiments?


Thanks,

Anna
--
Eng. Anna Procopio, Ph.D.
University "Magna Graecia" of Catanzaro 
email: anna.p...@unicz.it
skype: anna.procopio9

----------------------------------------------------------------------------------------------------------------------------------------------------------

PRIVACY: In ottemperanza con il nuovo Regolamento Europeo GDPR n. 679/2016, le informazioni contenute in questo messaggio sono riservate e il loro utilizzo è consentito esclusivamente al destinatario del messaggio. Qualora Lei non fosse la persona a cui il presente messaggio è destinato, La invitiamo a non leggere, copiare, inoltrare o salvare sul suo computer; qualora Lei avesse ricevuto il presente messaggio per errore ne dia immediata comunicazione con una e-mail al mittente e cancelli il messaggio. 

L’Amministrazione opera in conformità al nuovo Regolamento Europeo GDPR n. 679/2016. Per qualsiasi informazione a riguardo si prega di contattare l’indirizzo e-mail: dir...@unicz.it


PRIVACY: In accordance with the European Data Protecion Regulation (2016/679), the information contained in this e mail message is strictly confidential and intended for the use of the addressee only. If you are not the intended recipient, please do not read, copy, forward or store it on your computer; If you have received this message in error, please advise the sender immediately by e-mail and delete this message. 

The Administration operates in accordance with the European GDPR Regulation. For any information, please contact the e-mail address: dir...@unicz.it.

Diana El Assal

unread,
Jun 6, 2023, 6:26:20 AMJun 6
to cobra-...@googlegroups.com
Hi Anna,

Yes, one way would be to perform FBA then run a for loop to sequentially reduce the fluxes by e.g. 50% of the FBA flux. In some cases, this will result in infeasible solutions, so bear that in mind when you write the for loop.

Don't hesitate to ask if you have more questions. 

Best wishes, 

Diana
--

---
You received this message because you are subscribed to the Google Groups "COBRA Toolbox" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cobra-toolbox+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cobra-toolbox/CAKmzy8R-EPtpTRJK%2BEQbcDr7DdY8BzNeHtqMxQNLYHnpRrLt7Q%40mail.gmail.com.


--

Anna Procopio

unread,
Jun 6, 2023, 6:58:11 AMJun 6
to cobra-...@googlegroups.com
Ok. The fluxes associated to the metabolites of the reactions regulated by the gene that I want to investigate. It’s right? 

Thank you very much Diana, for your response and your time.

Best wishes,
Anna

To unsubscribe from this group and stop receiving emails from it, send an email to cobra-toolbo...@googlegroups.com.



--

--

---
You received this message because you are subscribed to the Google Groups "COBRA Toolbox" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cobra-toolbo...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cobra-toolbox/CALwnsfP%3D5fJ2Ay7N1%2BRB%3DFmg66NxjjwO7NNMoWobSYainDaefw%40mail.gmail.com.
--

Diana El Assal

unread,
Jun 6, 2023, 10:35:51 AMJun 6
to cobra-...@googlegroups.com
Hi Anna, 

Yes, you have to consider the genes that you want to knock down and reduce the fluxes of the reactions catalyzed by the encoded enzymes, based on GPR associations. Or you can do it for all reactions and extract the associated gene(s) that affect the objective function following sequential "knockdown" of all reactions in the model (using a for loop). 

What I normally do, is that I force the model to carry a 50% flux by setting the lower and upper bounds to 50% of the FBA flux. You can also perform this same in silico experiment by "overexpressing" the encoded enzyme. I suggest you use a minNorm to obtain unique solutions when using optimizeCbModel

Best wishes, 

Diana



--

                                                                                                

Diana Charles Jordan-El Assal, PhD


(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

Anna Procopio

unread,
Jun 6, 2023, 11:59:59 AMJun 6
to cobra-...@googlegroups.com
Perfect. 
Thanks again for the explanation Diana.


Best wishes,
Anna

Reply all
Reply to author
Forward
0 new messages