#437 Overexpression/Underexpression

[Lynzey Kujan]

Hello,

There seems to be no sequence ontology for Overexpression or Underexpression for variant trasncripts.

Overexpression of a transcript is a variant such that the amino acids of the trasncript are expressed more than others, despite all illustrated equally. In other words, it is a processing error due to the state of the other variants in the transcript.

Underexpression of a trasncript is a variant such that the amino acids of the trasncript are expressed less than others, despite all illustrated equally. In other words, it is a processing error due to the state of the other variants in the transcript.

Would you please add the two.

Thank you for your time,

Lynzey

[Karen Eilbeck]

Hi
We have moved this tracker to the github site as the sourceforge is being retired.
https://github.com/The-Sequence-Ontology/SO-Ontologies/issues

Your term requests look good and I will comment on github as I work on them
Cheers
Karen.

[Pankaj Jaiswal]

I think this is a molecular phenotype of the transcript isoform/gene and
not a sequence ontology feature. Reason is that it was measured based on
some observed value of # of aligned reads (RNA-Seq) or intensity of the
spot (microarray).

Pankaj

On 10/26/2015 10:15 AM, Karen Eilbeck wrote:

Hi
We have moved this tracker to the github site as the sourceforge is being retired.
https://github.com/The-Sequence-Ontology/SO-Ontologies/issues

Your term requests look good and I will comment on github as I work on them
Cheers
Karen.

---

[term-tracker:#437] Overexpression/Underexpression

Status: open
Group:
Created: Mon Oct 26, 2015 01:52 PM UTC by Lynzey Kujan
Last Updated: Mon Oct 26, 2015 01:52 PM UTC
Owner: nobody

Hello,

There seems to be no sequence ontology for Overexpression or Underexpression for variant trasncripts.

Overexpression of a transcript is a variant such that the amino acids of the trasncript are expressed more than others, despite all illustrated equally. In other words, it is a processing error due to the state of the other variants in the transcript.

Underexpression of a trasncript is a variant such that the amino acids of the trasncript are expressed less than others, despite all illustrated equally. In other words, it is a processing error due to the state of the other variants in the transcript.

Would you please add the two.

Thank you for your time,

Lynzey

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--
Pankaj Jaiswal, PhD
Associate Professor
Dept. of Botany and Plant Pathology
2082 Cordley Hall
Oregon State University
Corvallis, OR, 97331
USA

Ph.: +1-541-737-8471
Fax: +1-541-737-3573
email: jaiswalp@oregonstate.edu
Web: http://jaiswallab.cgrb.oregonstate.edu/

[Pankaj Jaiswal]

And the over/under expression is in comparison to some reference and
dependent on Genotype x Environment x Management/experiment-setup.

Pankaj

On 10/26/2015 12:27 PM, Jaiswal, Pankaj - OSU wrote:

I think this is a molecular phenotype of the transcript isoform/gene and
not a sequence ontology feature. Reason is that it was measured based on
some observed value of # of aligned reads (RNA-Seq) or intensity of the
spot (microarray).

Pankaj

On 10/26/2015 10:15 AM, Karen Eilbeck wrote:

Hi
We have moved this tracker to the github site as the sourceforge is
being retired.
https://github.com/The-Sequence-Ontology/SO-Ontologies/issues

Your term requests look good and I will comment on github as I work on
them
Cheers
Karen.

---

[term-tracker:#437] Overexpression/Underexpression

Status: open
Group:
Created: Mon Oct 26, 2015 01:52 PM UTC by Lynzey Kujan
Last Updated: Mon Oct 26, 2015 01:52 PM UTC
Owner: nobody

Hello,

There seems to be no sequence ontology for Overexpression or
Underexpression for variant trasncripts.

Overexpression of a transcript is a variant such that the amino acids
of the trasncript are expressed more than others, despite all
illustrated equally. In other words, it is a processing error due to
the state of the other variants in the transcript.

Underexpression of a trasncript is a variant such that the amino acids
of the trasncript are expressed less than others, despite all
illustrated equally. In other words, it is a processing error due to
the state of the other variants in the transcript.

Would you please add the two.

Thank you for your time,

Lynzey

---

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/song/term-tracker/437/

To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/

--
Pankaj Jaiswal, PhD
Associate Professor
Dept. of Botany and Plant Pathology
2082 Cordley Hall
Oregon State University
Corvallis, OR, 97331
USA

Ph.: +1-541-737-8471
Fax: +1-541-737-3573
email: jaiswalp@oregonstate.edu
Web: http://jaiswallab.cgrb.oregonstate.edu/