Asgruber at 14:56, 10 March 2016

2016-03-10T14:56:38Z

Asgruber: Created page with "fix bad characters new protein functions intestines --> filter high values, corr FPKM; right now we are getting a mixture of fed and non-fed when clustering. DEseq has al..."

2016-02-25T19:54:08Z

Created page with "fix bad characters new protein functions intestines --> filter high values, corr FPKM; right now we are getting a mixture of fed and non-fed when clustering. DEseq has al..."

New page

fix bad characters
new protein functions
intestines --> filter high values, corr FPKM; right now we are getting a mixture of fed and non-fed when clustering.
DEseq has already told us that clustering goes from fed vs non-fed

Ultimate goal is a term paper with intro, methods, and description on the candidate genes we found and why we decided on those.

Good genes to track down- transcription factors, transporters, anything in the signaling cascade.

FPKM- adjusted expression levels for length of gene

Today. Keep on looking for genes and smaller clusters. Is a smaller cluster necessarily advantageous? Don't we want a gene that turns on a lot of things?

Translation initiation protein:

I'm not having a ton of success, getting small clusters when prioritizing the type of gene first,

[http://gcat.davidson.edu/mediawiki-1.19.1/index.php/Ashlyn Ashlyn's Main Page]

← Older revision		Revision as of 14:56, 10 March 2016
Line 1:		Line 1:
−	~~fix~~ bad characters	+	== Classwork ==
−	new protein functions	+	Different groups in class will work on fixing bad characters and identifying new protein functions? (I'm confused by this)
−	~~intestines --> filter high values, corr FPKM; right now we are getting a mixture of fed and non-fed when clustering.~~
−	~~DEseq has already told us that clustering goes from fed vs non-fed~~
−
−	~~Ultimate goal is a term paper with intro, methods, and description on the candidate genes we found and why we decided on those.~~
−
−	~~Good genes to track down- transcription factors, transporters, anything in the signaling cascade.~~
−
−	~~FPKM- adjusted expression levels for length of gene~~
−
−	~~Today. Keep on looking for genes and smaller clusters. Is a smaller cluster necessarily advantageous~~? ~~Don't we want a gene that turns on a lot of things?~~
−
−	~~Translation initiation protein:~~
−
−
−	I'm ~~not having a ton of success, getting small clusters when prioritizing the type of gene first,~~

		+	As of late when working with the intestine samples, we are getting a mixture of fed and non-fed when clustering even though DEseq has already told us that clustering goes from fed vs. non-fed. Moving forward, we will play with the filter values and use the correction FPKM. <-- this doesn't sound right... talk to Elise and Kathryn. FPKM is the adjusted expression levels for the length of gene.

		+	Remember, the ultimate goal of this class is a term paper with an introduction, methods, and description of found candidate genes explaining what each candidate gene does and why we selected it. Good potential candidate genes include: transcription factors, transporters, and anything in the signaling cascade.


		+	In class today, we looked for genes belonging to smaller clusters. Other than a lot of trial and error and familiarizing myself with the programming and clustering process, I did not have significant success finding genes that belong to small clusters.


		+	==== Questions to Consider: ====
		+	*Is a smaller cluster necessarily advantageous considering that we want to find a gene that turns-on a lot of other genes?

February 25, 2016 - Revision history

Asgruber at 14:56, 10 March 2016

Asgruber: Created page with "fix bad characters new protein functions intestines --> filter high values, corr FPKM; right now we are getting a mixture of fed and non-fed when clustering. DEseq has al..."