Kwrigh35 Week 12 - Revision history

Kwrigh35: /* Emma and Katie's personal ideas on further research */ added a few more points (top three)

2017-11-21T07:57:50Z

‎Emma and Katie's personal ideas on further research: added a few more points (top three)

2017-11-21T07:46:04Z

‎Results of this study in comparison to the results of previous studies: added new section, personal ideas for future research

2017-11-21T07:44:18Z

‎Results: fixed syntax error

2017-11-21T07:43:33Z

‎Results: added more results

2017-11-21T07:40:28Z

added link to presentation

2017-11-21T07:22:33Z

‎Article Outline: added section on materials and methods, changed heading level of Microarray design, added info on preparation of yeast and probes

2017-11-21T06:51:59Z

‎Results of this study in comparison to the results of previous studies: added a response

2017-11-21T05:49:37Z

‎Results: added one bullet point before hierarchical cluster analysis

2017-11-21T05:47:15Z

‎Results: added first result bullet point and sub-points

2017-11-21T05:34:40Z

‎Experimental design of the microarray data: removed instructions

@@ Line 78: / Line 78: @@
 ====Emma and Katie's personal ideas on further research====
-*How different types of stresses lead to similar or different changes in gene expression (e.g. salinity, pressure, chemicals, etc)
+*It was somewhat frustrating that this paper made so many references to previous papers, and yet did not compare its results to very many.
-*If there is significant change in gene expression depending on the temperature used for cold shock (ie cold shock at 2°C, 4°C and 6°C and 8°C).
+*The paper also did not indicate what the authors wanted to pursue as far as future research
 ==Acknowledgements==

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 *TPS1 and TPS2 genes were found to have a smaller fold induction in this study compared to a previous study by Kandror et al in 2004.
 **This discrepancy may be explained by use of different carbon sources in the two studies.
 ==Acknowledgements==

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 **Genes involved in cell rescue, defense and virulence, and energy and metabolism were up-regulated
 **Genes involved in protein synthesis, binding functions, activity regulation and fate were down-regulated
-*Transcription of some genes go into
+*Transcription of some genes go into overdrive after cold shock, others don’t
-overdrive after cold shock, others don’t
+**Cold-shock causes up-regulation of genes that lead to
 *** Energy preservation and cold tolerance
 *** Membrane maintenance and permeability increases

@@ Line 56: / Line 56: @@
 **Then the expression profile of the yeast constantly exposed to 4&deg;C
 **And finally, with the least similar gene expression, is the yeast constantly exposed to 35&deg;C.
 ====Results of this study in comparison to the results of previous studies====

@@ Line 1: / Line 1: @@
 ==Electronic Notebook==
 ===New Terms===
 Make a list of at least 10 terms for which you did not know the definitions when you first read the article.  Define each of the terms and provide a citation for each term.

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 *It is also important to study the differences between organisms that have never been exposed to cold temperatures and organisms that have been grown in these cold conditions.  This will allow us to determine if/how well yeast can adapt to the cold.
-====Experimental design of the microarray data====
+====Methods and Materials====
 *The cDNA microarrays contained targets for 5,952 genes
 **cDNA microarray chip comes from "DNA Chip Research, Kanagawa, Japan"

← Older revision		Revision as of 06:51, 21 November 2017
Line 44:		Line 44:

	====Results of this study in comparison to the results of previous studies====		====Results of this study in comparison to the results of previous studies====
		+	The results of this study looked very '''similar''' to those of previous studies. Here are a couple of examples:
		+	*Genes encoding HSPs were induced by 4°C exposure. These genes were also observed to be induced at 0°C during a 2004 study of near-freezing response by Kang et al.
		+	*Trehalose synthesis was also shown to be important at low temperatures during a 2004 study by Kandror et al.
		+
		+	There are also some instances where the results of this study are '''different''' from previous ones. For example:
		+	*TPS1 and TPS2 genes were found to have a smaller fold induction in this study compared to a previous study by Kandror et al in 2004.
		+	**This discrepancy may be explained by use of different carbon sources in the two studies.

	==Acknowledgements==		==Acknowledgements==

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 ====Results====
 *Hierarchical cluster analysis can be used to determine which sets of data are most similar to each other.  The process begins by grouping the two most similar data sets together into a "cluster." Data sets are then added one-by-one to the initial cluster in order of similarity, until all data is categorized into one cluster. ''This technique revealed which time-points have the greatest similarity in gene expression.''
 **Hours 12 and 24 have the most similar gene-expression profile, and therefore are clustered together first.

← Older revision		Revision as of 05:47, 21 November 2017
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	====Results====		====Results====
		+	*Hierarchical cluster analysis can be used to determine which sets of data are most similar to each other. The process begins by grouping the two most similar data sets together into a "cluster." Data sets are then added one-by-one to the initial cluster in order of similarity, until all data is categorized into one cluster. ''This technique revealed which time-points have the greatest similarity in gene expression.''
		+	**Hours 12 and 24 have the most similar gene-expression profile, and therefore are clustered together first.
		+	**The next closest to this cluster is 48 hours, which can then be added to the 12/24h cluster form another, bigger cluster.
		+	**Hour 6 is the next closest to this cluster.
		+	**Then the expression profile of the yeast constantly exposed to 4°C
		+	**And finally, with the least similar gene expression, is the yeast constantly exposed to 35°C.
		+
	====Results of this study in comparison to the results of previous studies====		====Results of this study in comparison to the results of previous studies====

@@ Line 32: / Line 32: @@
 *20% of the data was used to calculate the Lowess fit at each point of a log-intensity vs log-ratio plot.  The resulting curve was used to adjust the control value for each measurement.
 *Multiple DNA microarray trial were run, and at least 5 independent cultures were used.
 *Genes with hypridization ratios &gt; 2.0 and &lt; 0.5 in at least 3 out of 5 experiments were considered up-regulated or down-regulate (respectively).
 ====Results====