February 16, 2016 - Revision history

Asgruber at 14:43, 9 March 2016

2016-03-09T14:43:58Z

Asgruber at 14:43, 9 March 2016

2016-03-09T14:43:09Z

Asgruber at 14:42, 9 March 2016

2016-03-09T14:42:37Z

Asgruber: /* Identified Genes */

2016-03-09T14:37:43Z

‎Identified Genes

Asgruber at 14:37, 9 March 2016

2016-03-09T14:37:28Z

Asgruber at 14:36, 9 March 2016

2016-03-09T14:36:29Z

Asgruber at 14:08, 9 March 2016

2016-03-09T14:08:20Z

Asgruber at 19:54, 16 February 2016

2016-02-16T19:54:15Z

Asgruber at 19:49, 16 February 2016

2016-02-16T19:49:46Z

Asgruber: Created page with "== Classwork == Still trying to do searches by gene ontology terms Still trying to figure out if our organ samples are good samples (using DEseq?) **DEseq = different..."

2016-02-16T19:49:07Z

Created page with "== Classwork == *Still trying to do searches by gene ontology terms *Still trying to figure out if our organ samples are good samples (using DEseq?) **DEseq = different..."

New page

== Classwork ==

*Still trying to do searches by gene ontology terms
*Still trying to figure out if our organ samples are good samples (using DEseq?)
**DEseq = differential expression of RNA-seq
**Which ones should we continue on with

David wasn't great and only works for humans and needs gene I.D.'s for Python genes which don't exist

DEseq notes- reports the number of reads assigned to each gene

"To
contrast two conditions, e.g., to see whether there is di�erential expression between conditions\untreated"and\treated",
we simply call the function
nbinomTest
. It performs the tests as described in [1] and returns a data frame with the
p
values and other useful information"
Need to test things in replicate when dealing with a biological experiment.
Personally, I do not have the programming or genomics background to make sense of the DEseq link provided in the syllabus.

LOOK FOR HOUSE KEEPING GENE:
*Started by looking in Intestine Result folder in BIO343 folder.
Intestine 4 fed:
*searched transcription factor, then googled each one to find out what they do
**transcription factor_2 Gallus Gallus
***COUP transcription factor 2
****necessary for expression of chicken ovalbumin gene
****biological process is negative regulation of endopeptidase activity

Intestine Blast interesting genes highlighted in red- looking at these to figure out if we can use them/ if they are only in the intestine/ if they can help us verify our tissue sample.
For Thursday, share what we've found (I don't think I've found anything), BUT we are trying to verify all 12 samples to make sure which ones we should carry on with.
Dr. Campbell and Dr. Heyer compared liver fed to no_fed and found 3 transcription factors, then they want to change the way it clusters and look at all the genes that correlate with those transcription factors (supervised cluster).
***"species = human"

← Older revision		Revision as of 14:43, 9 March 2016
Line 27:		Line 27:
	'''''Moving forward, after tissues are verified we want to identify transcription factors and research the genes that correlate with the identified transcription factors using supervised clustering.'''''		'''''Moving forward, after tissues are verified we want to identify transcription factors and research the genes that correlate with the identified transcription factors using supervised clustering.'''''

−
−
−
−	*Note: Ashlyn left class early this day to travel for Track & Field competition.



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

← Older revision		Revision as of 14:43, 9 March 2016
Line 20:		Line 20:


−	Reference [http://gcat.davidson.edu/mediawiki-1.19.1/index.php/Notes_2/16/16 Kathryn's ~~February~~ 16~~, 2016~~ notes] for a more complete list of genes to verify tissue samples.	+	Reference [http://gcat.davidson.edu/mediawiki-1.19.1/index.php/Notes_2/16/16 Kathryn's 2/16/16 notes] for a more complete list of genes to verify tissue samples.

@@ Line 17: / Line 17: @@
 **Belongs to the COUP transcription factor 2 group.
 **Necessary for expression of chicken ovalbumin gene.
 **MAKE NOTE OF WHETHER IT WAS UP OR DOWN REGULATED!
-'''''Moving forward, after tissues are verified we want to identify transcription factors and research the genes that correlate with the identified transcription factors using supervised clustering.'''''
+Reference [http://gcat.davidson.edu/mediawiki-1.19.1/index.php/Notes_2/16/16 Kathryn's February 16, 2016 notes] for a more complete list of genes to verify tissue samples.
-Make notes about referencing Kathryn's page for gene descriptions and housekeeping genes.
 [http://gcat.davidson.edu/mediawiki-1.19.1/index.php/Ashlyn Ashlyn's Main Page]

@@ Line 11: / Line 11: @@
-=== Identified Genes ===
+=== Identified Genes: ===
 '''Intestine 4 fed'''
 *Transcription factor_2 Gallus gallus

@@ Line 11: / Line 11: @@
-==== Identified Genes ====
+=== Identified Genes ===
-=== Intestine 4 fed ====
+'''Intestine 4 fed'''
 *Transcription factor_2 Gallus gallus
 **Biological process: negative regulation of endopeptidase activity

@@ Line 1: / Line 1: @@
 == Classwork ==
-*Still trying to do searches by gene ontology terms
+Currently, the class is still trying to do gene ontology searches. The class is also still trying to verify organ samples and determine if any samples should be discarded as our research progresses. We also discussed in groups DEseq and learned that DEseq allows researchers to contrast two conditions and determine the differences in expression between the conditions. Ideally, when dealing with a biological experiment, conditions would be tested in replicate. Furthermore, I, personally, did not have the programming or genomics background to make sense of most of the content in the DEseq link provided by the syllabus.
-DEseq notes- reports the number of reads assigned to each gene
+== Gene Search ==
-"To
+We began our house-keeping gene search by looking through genes in the IntestineResult data in the BIO343 folder. From the Intestine Blast, interesting genes were highlighted in red and were a good starting point for genes that could help us verify the tissue samples. After identifying a gene of interest, we searched the gene in google to learn more about its function and other characteristics. The goal of our gene search is to verify all six intestine samples in order to be confident moving forward with them.
-contrast two conditions, e.g., to see whether there is di�erential expression between conditions\untreated"and\treated",
-we simply call the function
-nbinomTest
-.  It performs the tests as described in [1] and returns a data frame with the
+==== Identified Genes ====
+=== Intestine 4 fed ====
-values and other useful information"
+*Transcription factor_2 Gallus gallus
-Need to test things in replicate when dealing with a biological experiment.
+**Biological process: negative regulation of endopeptidase activity
-Personally, I do not have the programming or genomics background to make sense of the DEseq link provided in the syllabus.
+**Belongs to the COUP transcription factor 2 group.
 Make notes about referencing Kathryn's page for gene descriptions and housekeeping genes.

← Older revision		Revision as of 14:08, 9 March 2016
Line 7:		Line 7:


−	~~David wasn't great and only works for humans and needs gene I.D.'s for Python genes which don't exist~~

	DEseq notes- reports the number of reads assigned to each gene		DEseq notes- reports the number of reads assigned to each gene

← Older revision		Revision as of 19:54, 16 February 2016
Line 35:		Line 35:
	***"species = human"		***"species = human"

		+	Make notes about referencing Kathryn's page for gene descriptions and housekeeping genes.



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

@@ Line 33: / Line 33: @@
 For Thursday, share what we've found (I don't think I've found anything), BUT we are trying to verify all 12 samples to make sure which ones we should carry on with.
 Dr. Campbell and Dr. Heyer compared liver fed to no_fed and found 3 transcription factors, then they want to change the way it clusters and look at all the genes that correlate with those transcription factors (supervised cluster).
 ***"species = human"

February 16, 2016 - Revision history

Asgruber at 14:43, 9 March 2016

Asgruber at 14:43, 9 March 2016

Asgruber at 14:42, 9 March 2016

Asgruber: /* Identified Genes */

Asgruber at 14:37, 9 March 2016

Asgruber at 14:36, 9 March 2016

Asgruber at 14:08, 9 March 2016

Asgruber at 19:54, 16 February 2016

Asgruber at 19:49, 16 February 2016

Asgruber: Created page with "== Classwork == *Still trying to do searches by gene ontology terms *Still trying to figure out if our organ samples are good samples (using DEseq?) **DEseq = different..."

Asgruber: Created page with "== Classwork == Still trying to do searches by gene ontology terms Still trying to figure out if our organ samples are good samples (using DEseq?) **DEseq = different..."