Aporras1 Week 10 - Revision history

Aporras1: /* Summary Paragraph */ summary of assignment

2017-11-30T04:49:42Z

‎Summary Paragraph: summary of assignment

Aporras1: summary header

2017-11-30T01:24:49Z

summary header

Aporras1: /* Deliverable Files */ uploaded txt file

2017-11-30T01:24:01Z

‎Deliverable Files: uploaded txt file

Aporras1: /* Deliverable Files */ formatting

2017-11-30T01:21:34Z

‎Deliverable Files: formatting

Aporras1: /* Deliverable Files */ uploaded stem spreadsheet

2017-11-30T01:20:46Z

‎Deliverable Files: uploaded stem spreadsheet

Aporras1: /* Electronic Notebook */ genes left fix

2017-11-30T01:13:30Z

‎Electronic Notebook: genes left fix

Aporras1: /* Acknowledgements */ week 10 modified

2017-11-30T00:55:01Z

‎Acknowledgements: week 10 modified

Aporras1: /* References */ references to GO term definitions

2017-11-30T00:49:16Z

‎References: references to GO term definitions

Aporras1: /* Electronic Notebook */ interpretation of GO terms

2017-11-30T00:38:12Z

‎Electronic Notebook: interpretation of GO terms

Aporras1: /* Electronic Notebook */ definitions of GO terms

2017-11-30T00:15:26Z

‎Electronic Notebook: definitions of GO terms

← Older revision		Revision as of 04:49, 30 November 2017
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	==Summary Paragraph==		==Summary Paragraph==
		+	In week 10's assignment we were only able to complete up until the analysis and interpretation of the stem results. However, we still gained a thorough understanding of the use of stem to analyze cold shock response in saccharomyces cerevisiae inasmuch that I selected a profile, profile 22, to specifically find genes and GO terms which were most significant in change of expression during cold shock. These specific GO terms defined prior in this assignment are areas of the cell in which energy may be direct towards or away from in order to respond to the stimulation. Specifically,the yeast may be redirecting energy away from processes which aren't necessary in stress response and towards expression of genes which aid in responding to the stress. As we've learned in recent class presentations, there are fewer genes expressed in response to cold shock compared to heat shock and there seems to be a trend towards downregulation of genes.

	==Deliverable Files==		==Deliverable Files==

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 ##*** '''Glucose 6-phosphate metabolic process GO:0051156''' - "The chemical reactions and pathways involving glucose 6-phosphate, a monophosphorylated derivative of glucose with the phosphate group attached to C-6."
 ## '''Why does the cell react to cold shock by changing the expression of genes associated with these GO terms?''' The cell reacts to cold shock by changing expression of genes associated with these go terms in order to adapt to the environmental stress. The stress causes the cell to react and divert energy from processes that aren't necessary to survive in order to use that energy towards responding to the cold stress.
 ==Deliverable Files==

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 #[[Media:AP dZAP1 STEM Profiles and Powerpoint.zip]]
 #[[Media:AP dZAP1 stem.xlsx]]
 ==Acknowledgements==

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 ==Deliverable Files==
 #[[Media:AP dZAP1 STEM Profiles and Powerpoint.zip]]
-#[[Media:AP dZAP1 stem.xlsx
+#[[Media:AP dZAP1 stem.xlsx]]
 ==Acknowledgements==

@@ Line 94: / Line 94: @@
 ==Deliverable Files==
 #[[Media:AP dZAP1 STEM Profiles and Powerpoint.zip]]
 ==Acknowledgements==

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 #** Changed leftmost column header "Master_Index" to "SPOT".  Changed column B "ID" to "Gene Symbol".  Deleted the column named "Standard_Name".
 #** Filtered the data on the B-H corrected p value to be > 0.05 (that's '''greater than''' in this case).
-#*** Selected all of the rows (except for the header row) and deleted the rows by right-clicking and choosing "Delete Row" from the context menu.  Undid the filter.  This ensured that I would cluster only the genes with a "significant" change in expression and not the noise.  '''''Record the number of genes left in your electronic notebook.''''' 1775 genes were left.
+#*** Selected all of the rows (except for the header row) and deleted the rows by right-clicking and choosing "Delete Row" from the context menu.  Undid the filter.  This ensured that I would cluster only the genes with a "significant" change in expression and not the noise.  '''''Record the number of genes left in your electronic notebook.''''' 1785 genes were left.
 #** Deleted all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).
 #** Renamed the data columns with just the time and units (for example, 15m, 30m, etc.).

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 #Worked in class with [[User:Kwrigh35|Katie Wright]] to discuss any questions we had throughout the process of completing the Week 10 assignment.
 #Recieved help from both [[User:Dondi|Dondi]] and [[User:Kdahlquist|Dr. Dahlquist]] during the allotted class period.
 '''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

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 ==References==
-#LMU BioDB 2017. (2017). Week 10. Retrieved October 31, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
+# LMU BioDB 2017. (2017). Week 10. Retrieved October 31, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
 [[Category:Journal Entry]]

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 ##** In the results page, clicked on the button that says "Link to detailed information about actin binding".
 ##** The definition was found on the next results page.
-##*** '''Actin binding GO:0003779''' -
+##*** '''Actin binding GO:0003779''' - "Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments."
 ##** Copied and paste the ID GO:0098805 into the search field at center top of the page called "Search GO Data".
 ##** In the results page, clicked on the button that says "Link to detailed information about whole membrane".
 ##** The definition was found on the next results page.
-##*** '''Whole membrane GO:0098805''' -
+##*** '''Whole membrane GO:0098805''' - "Any lipid bilayer that completely encloses some structure, and all the proteins embedded in it or attached to it. Examples include the plasma membrane and most organelle membranes."
 ##** Copied and paste the ID GO:0005739 into the search field at center top of the page called "Search GO Data".
 ##** In the results page, clicked on the button that says "Link to detailed information about mitochondrian".
 ##** The definition was found on the next results page.
-##*** '''Mitochondrian GO:0005739''' -
+##*** '''Mitochondrian GO:0005739''' - "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration."
 ##** Copied and paste the ID GO:0098754 into the search field at center top of the page called "Search GO Data".
 ##** In the results page, clicked on the button that says "Link to detailed information about detoxification".
 ##** The definition was found on the next results page.
-##*** '''Detoxification GO:0098754''' -
+##*** '''Detoxification GO:0098754''' - "Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance."
 ##** Copied and paste the ID GO:0008092 into the search field at center top of the page called "Search GO Data".
 ##** In the results page, clicked on the button that says "Link to detailed information about cytoskeletal protein binding".
 ##** The definition was found on the next results page.
-##*** '''Cytoskeletal protein binding GO:0008092''' -
+##*** '''Cytoskeletal protein binding GO:0008092''' - "Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton)."
 ##** Copied and paste the ID GO:0051156 into the search field at center top of the page called "Search GO Data".
 ##** In the results page, clicked on the button that says "Link to detailed information about glucose 6-phosphate metabolic process".
 ##** The definition was found on the next results page.
-##*** '''Glucose 6-phosphate metabolic process GO:0051156''' -
+##*** '''Glucose 6-phosphate metabolic process GO:0051156''' - "The chemical reactions and pathways involving glucose 6-phosphate, a monophosphorylated derivative of glucose with the phosphate group attached to C-6."
 ==Deliverable Files==