February 18, 2016 - Revision history

Asgruber at 15:11, 9 March 2016

2016-03-09T15:11:47Z

Asgruber at 15:07, 9 March 2016

2016-03-09T15:07:22Z

Asgruber at 15:00, 9 March 2016

2016-03-09T15:00:02Z

Asgruber at 19:11, 18 February 2016

2016-02-18T19:11:57Z

Asgruber: Created page with "Dr. C and Dr. Heyer made cool progress. We did not do Euclidian distance, we looked at CORRElATION, we can also do absolute value. p value = 0.01 instead of 0.05 so that we ..."

2016-02-18T19:05:38Z

Created page with "Dr. C and Dr. Heyer made cool progress. We did not do Euclidian distance, we looked at CORRElATION, we can also do absolute value. p value = 0.01 instead of 0.05 so that we ..."

New page

Dr. C and Dr. Heyer made cool progress.
We did not do Euclidian distance, we looked at CORRElATION, we can also do absolute value.
p value = 0.01 instead of 0.05 so that we get a shorter list of genes. Document has code on it.
There is a code where you can find gene names. "write.csv(colnames(carp).... if there is a seed gene we want genes most correlated to that one. Theres a lot of really good candidate genes!
Transcription factors are not always transcribed in high quanities becuase you don't need a lot... So look for change (on vs. off) not just quantity of expression.
t in code = transforming/transposing x and y axis.

Tae sequences put them in Blast to Go- put in formated listed of sequences then it runs it through mapping. Sequence based method...
Other group taking gene names from file and pair names of genes in gene file to gene ontology terms. Name based method...

All 6 are good liver samples. We still need to identify/verify intestine samples 3 and 6. Look in excel sheet Kathryn shared. Blasting over represented genes gave us genes. Look at and cite Kathryn's page. Google names on list of housekeeping genes and see if we can verify/decode/match differences in names to verify tissue samples.

Housekeeping genes in Pythons: NHE3 is a sodium transporter in intestinal membrane. Let's see if it matches up with one of our samples. [http://www.annualreviews.org/doi/full/10.1146/annurev.physiol.67.031103.153004 NHE3 article]

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

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 All six liver samples are viable. However, we still need to verify intestine samples 3 and 6.
-After attaining a list of genes from a previous blast of over represent genes, we tried to match these genes with genes in intestine samples 3 and 6. We googled the names of housekeeping genes from [ Kathryn's list of housekeeping genes] to see if we can decode the differences in gene identifications and match them to genes that would verify our tissue samples.  As we continued our gene search, we remembered that transcription factors are not always transcribed in high quantities so we must look for change in expression (on vs. off) instead of only looking at quantity of expression.
+After attaining a list of genes from a previous blast of over represent genes, we tried to match these genes with genes in intestine samples 3 and 6. We googled the names of housekeeping genes from [http://gcat.davidson.edu/mediawiki-1.19.1/index.php/Notes_2/16/16 Kathryn's list of housekeeping genes] to see if we can decode the differences in gene identifications and match them to genes that would verify our tissue samples. We also attempted to find housekeeping genes given the list of genes in Castoe et al. (2013). As we continued our gene search, we remembered that transcription factors are not always transcribed in high quantities so we must look for change in expression (on vs. off) instead of only looking at quantity of expression.
-Housekeeping genes in Pythons:  NHE3 is a sodium transporter in intestinal membrane. Let's see if it matches up with one of our samples. [http://www.annualreviews.org/doi/full/10.1146/annurev.physiol.67.031103.153004  NHE3 article]
+=== Identified Genes: ===

@@ Line 3: / Line 3: @@
 Dr. Campbell and Dr. Heyer made significant progress on coding work for correlation. They changed the p-value from 0.05 to 0.01 so that R-Studio generates a shorter list of genes. (FIND DOCUMENT WITH THE CODE ON IT). Dr. Campbell and Dr. Heyer also mentioned a code that allows us to find gene names, "write.csv(colnames(carp)..." We want to use this code to find a seed gene, and then find genes most correlated to that seed gene.
-As we began our gene search, we remembered that transcription factors are not always transcribed in high quantities so we must look for change in expression (on vs. off) instead of only looking at quantity of expression.
+Other groups in the class are working formatting sequence lists. One group is using Blast 2Go while another group is using gene names from a file and pairing them with gene ontology terms to format sequences with a sequence-based method or name-based method, respectively.
 ''Coding Notes:''
 *"t" in code = transforming/transposing x and y axis.
 Housekeeping genes in Pythons:  NHE3 is a sodium transporter in intestinal membrane. Let's see if it matches up with one of our samples. [http://www.annualreviews.org/doi/full/10.1146/annurev.physiol.67.031103.153004  NHE3 article]
@@ Line 21: / Line 24: @@
-'''Note: Ashlyn left class early this day to travel for Track & Field competition.'''
+''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]

← Older revision		Revision as of 19:11, 18 February 2016
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	Housekeeping genes in Pythons: NHE3 is a sodium transporter in intestinal membrane. Let's see if it matches up with one of our samples. [http://www.annualreviews.org/doi/full/10.1146/annurev.physiol.67.031103.153004 NHE3 article]		Housekeeping genes in Pythons: NHE3 is a sodium transporter in intestinal membrane. Let's see if it matches up with one of our samples. [http://www.annualreviews.org/doi/full/10.1146/annurev.physiol.67.031103.153004 NHE3 article]

		+
		+	Also look for housekeeping genes given in Castoe et all (2013). We think they provide housekeeping genes

@@ Line 1: / Line 1: @@
-Dr. C and Dr. Heyer made cool progress.
+== Classwork ==
-We did not do Euclidian distance, we looked at CORRElATION, we can also do absolute value.
-p value = 0.01 instead of 0.05 so that we get a shorter list of genes.  Document has code on it.
+Dr. Campbell and Dr. Heyer made significant progress on coding work for correlation. They changed the p-value from 0.05 to 0.01 so that R-Studio generates a shorter list of genes. (FIND DOCUMENT WITH THE CODE ON IT). Dr. Campbell and Dr. Heyer also mentioned a code that allows us to find gene names, "write.csv(colnames(carp)..." We want to use this code to find a seed gene, and then find genes most correlated to that seed gene.
-There is a code where you can find gene names. "write.csv(colnames(carp).... if there is a seed gene we want genes most correlated to that one. Theres a lot of really good candidate genes!
-Transcription factors are not always transcribed in high quanities becuase you don't need a lot... So look for change (on vs. off) not just quantity of expression.
+As we began our gene search, we remembered that transcription factors are not always transcribed in high quantities so we must look for change in expression (on vs. off) instead of only looking at quantity of expression.
 t in code = transforming/transposing x and y axis.
 All 6 are good liver samples. We still need to identify/verify intestine samples 3 and 6. Look in excel sheet Kathryn shared. Blasting over represented genes gave us genes. Look at and cite Kathryn's page. Google names on list of housekeeping genes and see if we can verify/decode/match differences in names to verify tissue samples.
@@ Line 18: / Line 21: @@
 [http://gcat.davidson.edu/mediawiki-1.19.1/index.php/Ashlyn Ashlyn's Main Page]