Emmatyrnauer Week 10 - Revision history

Kdahlquist: /* Files */ link to YEASTRACT results

2017-11-30T23:03:20Z

‎Files: link to YEASTRACT results

Emmatyrnauer: /* Microarray Data Analysis Part 2: "High-level Analysis" */ fixing incorrect answers

2017-11-21T02:29:58Z

‎Microarray Data Analysis Part 2: "High-level Analysis": fixing incorrect answers

Emmatyrnauer: /* Electronic Notebook */ adding to conclusion

2017-11-20T00:03:00Z

‎Electronic Notebook: adding to conclusion

Emmatyrnauer: /* Acknowledgements */ typo

2017-11-19T23:47:46Z

‎Acknowledgements: typo

Emmatyrnauer: /* Acknowledgements */ typo

2017-11-19T23:46:57Z

‎Acknowledgements: typo

Emmatyrnauer: adding acknowledgments and references

2017-11-19T23:46:25Z

adding acknowledgments and references

Emmatyrnauer: /* Microarray Data Analysis Part 2: "High-level Analysis" */ typo

2017-11-19T23:15:15Z

‎Microarray Data Analysis Part 2: "High-level Analysis": typo

Emmatyrnauer: /* Electronic Notebook */ adding why cell might react to cold shock by changing expression of genes

2017-11-19T23:14:09Z

‎Electronic Notebook: adding why cell might react to cold shock by changing expression of genes

Emmatyrnauer: /* Electronic Notebook */ adding go id's and changing a term

2017-11-19T23:08:07Z

‎Electronic Notebook: adding go id's and changing a term

Emmatyrnauer: /* Electronic Notebook */ editing question answers to correspond to new graphs after bh correction

2017-11-19T22:54:16Z

‎Electronic Notebook: editing question answers to correspond to new graphs after bh correction

@@ Line 62: / Line 62: @@
 #Updated powerpoint presentation: [[Media:Wt_profileimage_presentation_emmat.pptx]]
 #File used to run stem, gene list tables, GO list tables: [[Media:Week10_filesforstem_wildtype_emmat.zip‎]]
 ====Conclusion====

@@ Line 37: / Line 37: @@
 ## I selected one of the profiles I saved in the previous step for further interpretation of the data.
 ##* '''''Why did you select this profile?  In other words, why was it interesting to you?'''''
-##**<span style="color:red">I chose profile 45 because it shows a general trend of up regulation of genes at the cold shock time points (in other words, there was more regulation--less expression of these genes).</span>
+##**<span style="color:red">I chose profile 45 because it shows a general trend of up regulation of genes at the cold shock time point.</span>
 ##* '''''How many genes belong to this profile?'''''
 ##**<span style="color:red">549 genes belong to this profile.</span>
@@ Line 57: / Line 57: @@
 ##***<span style="color:red">'''nucleoplasm''' (GO:0005654): That part of the nuclear content other than the chromosomes or the nucleolus.</span> [http://amigo.geneontology.org/amigo/term/GO:0005654]
 ##***<span style="color:red">'''ribosomal subunit export from nucleus''' (GO:0000054): The directed movement of a ribosomal subunit from the nucleus into the cytoplasm. </span> [http://amigo.geneontology.org/amigo/term/GO:0000054]
-##**** '''Why does the cell react to cold shock by changing the expression of genes associated with these GO terms?''' The activity of these genes associated with these GO terms may slow in order to conserve energy after exposure to cold shock. This is because these cellular components may not be carrying out their normal functions (or at the same pace) in a highly-stressed environment compared to standard conditions.
+##**** '''Why does the cell react to cold shock by changing the expression of genes associated with these GO terms?''' The activity of these genes associated with these GO terms may increase to maintain viability of the cell in a highly-stressed environment. Furthermore, these genes may increase in expression to allow for greater efficiency of the cell during harsh conditions so that unnecessary energy is not expended.
 ====Files====
 #Updated excel spreadsheet: [[Media:Wt_Microarraydata_ET.zip]]
@@ Line 64: / Line 64: @@
 ====Conclusion====
-For the assignment this week, we did clustering and GO term enrichment with STEM, downloaded and ran the STEM software using an updated excel spreadsheet, obtained figures and results from the software, and analyzed and interpreted the STEM results. A new worksheet was created in the excel workbook from week 8 that involved renaming and filtering data from the wt_ANOVA worksheet. Using this updated file, STEM created figures and tables representing clusters/profiles of genes with similar responses in terms of expression following cold shock. One profile was chosen (45) for further analysis in terms of the identification of genes associated with different p-values within the profile, and 6 GO terms were selected from the filtered list of corrected p<0.05 and looked up with http://geneontology.org. Based on the GO terms that were designated for each cluster, I hypothesize that genes which code for parts of the cell that are utilized for normal function during standard conditions may be unregulated to conserve energy. On the other hand, genes which code for parts of the cell which are beneficial for survival during extreme conditions, may be expressed more (that is, down regulated) when exposed to cold shock.
+For the assignment this week, we did clustering and GO term enrichment with STEM, downloaded and ran the STEM software using an updated excel spreadsheet, obtained figures and results from the software, and analyzed and interpreted the STEM results. A new worksheet was created in the excel workbook from week 8 that involved renaming and filtering data from the wt_ANOVA worksheet. Using this updated file, STEM created figures and tables representing clusters/profiles of genes with similar responses in terms of expression following cold shock. One profile was chosen (45) for further analysis in terms of the identification of genes associated with different p-values within the profile, and 6 GO terms were selected from the filtered list of corrected p<0.05 and looked up with http://geneontology.org. Based on the GO terms that were designated for each cluster, I hypothesize that genes which code for parts of the cell which are needed for cell survival/cell rescue will be upregulated. On the other hand, genes involved in processes that aren't required for cell survival may be downregulated to conserve energy.
 ==Acknowledgements==

@@ Line 57: / Line 57: @@
 ##***<span style="color:red">'''nucleoplasm''' (GO:0005654): That part of the nuclear content other than the chromosomes or the nucleolus.</span> [http://amigo.geneontology.org/amigo/term/GO:0005654]
 ##***<span style="color:red">'''ribosomal subunit export from nucleus''' (GO:0000054): The directed movement of a ribosomal subunit from the nucleus into the cytoplasm. </span> [http://amigo.geneontology.org/amigo/term/GO:0000054]
-##**** Why does the cell react to cold shock by changing the expression of genes associated with these GO terms? The activity of these genes associated with these GO terms may slow in order to conserve energy after exposure to cold shock. This is because these cellular components may not be carrying out their normal functions (or at the same pace) in a highly-stressed environment compared to standard conditions.
+##**** '''Why does the cell react to cold shock by changing the expression of genes associated with these GO terms?''' The activity of these genes associated with these GO terms may slow in order to conserve energy after exposure to cold shock. This is because these cellular components may not be carrying out their normal functions (or at the same pace) in a highly-stressed environment compared to standard conditions.
 ====Files====
 #Updated excel spreadsheet: [[Media:Wt_Microarraydata_ET.zip]]
@@ Line 64: / Line 64: @@
 ====Conclusion====
-For the assignment this week, we did clustering and GO term enrichment with STEM, downloaded and ran the STEM software using an updated excel spreadsheet, obtained figures and results from the software, and analyzed and interpreted the STEM results. A new worksheet was created in the excel workbook from week 8 that involved renaming and filtering data from the wt_ANOVA worksheet. Using this updated file, STEM created figures and tables representing clusters/profiles of genes with similar responses in terms of expression following cold shock. One profile was chosen (45) for further analysis in terms of the identification of genes associated with different p-values within the profile, and 6 GO terms were selected from the filtered list of corrected p<0.05 and looked up with http://geneontology.org.
+For the assignment this week, we did clustering and GO term enrichment with STEM, downloaded and ran the STEM software using an updated excel spreadsheet, obtained figures and results from the software, and analyzed and interpreted the STEM results. A new worksheet was created in the excel workbook from week 8 that involved renaming and filtering data from the wt_ANOVA worksheet. Using this updated file, STEM created figures and tables representing clusters/profiles of genes with similar responses in terms of expression following cold shock. One profile was chosen (45) for further analysis in terms of the identification of genes associated with different p-values within the profile, and 6 GO terms were selected from the filtered list of corrected p<0.05 and looked up with http://geneontology.org. Based on the GO terms that were designated for each cluster, I hypothesize that genes which code for parts of the cell that are utilized for normal function during standard conditions may be unregulated to conserve energy. On the other hand, genes which code for parts of the cell which are beneficial for survival during extreme conditions, may be expressed more (that is, down regulated) when exposed to cold shock.
 ==Acknowledgements==

@@ Line 69: / Line 69: @@
 #I worked with my homework partner [[User:cazinge|Eddie Azinge]] during class and over text.
 #Dr. Dahlquist for teaching and assisting us with the data analysis
-# I copied and modified the instructions from the [[https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10 Week 10 Assignment]] page.
+# I copied and modified the instructions from the [[Week 10]] assignment page.
 While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
 [[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 15:14, 31 October 2017 (PDT)

@@ Line 69: / Line 69: @@
 #I worked with my homework partner [[User:cazinge|Eddie Azinge]] during class and over text.
 #Dr. Dahlquist for teaching and assisting us with the data analysis
-# I copied and modified the instructions from the [[https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10 | Week 10 Assignment]] page.
+# I copied and modified the instructions from the [[https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10 Week 10 Assignment]] page.
 While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
 [[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 15:14, 31 October 2017 (PDT)

@@ Line 55: / Line 55: @@
 ##***<span style="color:red">'''ncRNA catabolic process''' (GO:0034661): The chemical reactions and pathways resulting in the breakdown of non-coding RNA transcripts (ncRNAs). Includes the breakdown of cryptic unstable transcripts</span> [http://amigo.geneontology.org/amigo/term/GO:0034661]
 ##***<span style="color:red">'''intracellular membrane-bounded organelle''' (GO:0043231): Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane</span> [http://amigo.geneontology.org/amigo/term/GO:0043231]
-##***<span style="color:red">'''nucleoplasm''' (GO:0005654): That part of the nuclear content other than the chromosomes or the nucleolus.</span> [http://amigo.geneontology.org/amigo/term/GO:0006399]
+##***<span style="color:red">'''nucleoplasm''' (GO:0005654): That part of the nuclear content other than the chromosomes or the nucleolus.</span> [http://amigo.geneontology.org/amigo/term/GO:0005654]
 ##***<span style="color:red">'''ribosomal subunit export from nucleus''' (GO:0000054): The directed movement of a ribosomal subunit from the nucleus into the cytoplasm. </span> [http://amigo.geneontology.org/amigo/term/GO:0000054]
 ##**** Why does the cell react to cold shock by changing the expression of genes associated with these GO terms? The activity of these genes associated with these GO terms may slow in order to conserve energy after exposure to cold shock. This is because these cellular components may not be carrying out their normal functions (or at the same pace) in a highly-stressed environment compared to standard conditions.
@@ Line 69: / Line 69: @@
 #I worked with my homework partner [[User:cazinge|Eddie Azinge]] during class and over text.
 #Dr. Dahlquist for teaching and assisting us with the data analysis
 While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
 [[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 15:14, 31 October 2017 (PDT)
 ==References==
-#Gene Ontology Consortium. (2017). The Gene Ontology. Retrieved November 6, 2017, from http://geneontology.org
+#Gene Ontology Consortium. (2017). The Gene Ontology. Retrieved November 19, 2017, from http://geneontology.org
-#LMU BioDB 2017. (2017). Week 10. Retrieved November 4, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
+#*Ribosome assembly. The Gene Ontology. Retrieved November 19, 2017, from http://amigo.geneontology.org/amigo/term/GO:0042255
 {{Emmatyrnauer}}

@@ Line 44: / Line 44: @@
 ##* '''''What is the p value for the enrichment of genes in this profile?''''' (This p value determines whether the number of genes that show this particular expression profile across the time points is significantly more than expected.)
 ##**<span style="color:red">0.00 is the p-value for the enrichment of genes in this profile.</span>
-##* I opened the GO list file I saved for this profile in Excel.  This list shows all of the Gene Ontology terms that are associated with genes that fit this profile.  I selected the third row and then chose from the menu Data > Filter > Autofilter.  I filtered on the "p-value" column to show only GO terms that have a p value of < 0.05.  '''''How many GO terms are associated with this profile at p < 0.05?''''' <span style="color:red">247 GO terms are associated with profile 45. </span> The GO list also has a column called "Corrected p-value".  This correction is needed because the software has performed thousands of significance tests.  I filtered on the "Corrected p-value" column to show only GO terms that have a corrected p value of < 0.05.  '''''How many GO terms are associated with this profile with a corrected p value < 0.05?''''' <span style="color:red">28 GO terms are associated with profile 45 with a corrected p value < 0.05.</span>
+##* I opened the GO list file I saved for this profile in Excel.  This list shows all of the Gene Ontology terms that are associated with genes that fit this profile.  I selected the third row and then chose from the menu Data > Filter > Autofilter.  I filtered on the "p-value" column to show only GO terms that have a p value of < 0.05.  '''''How many GO terms are associated with this profile at p < 0.05?''''' <span style="color:red">240 GO terms are associated with profile 45 at p<0.05. </span> The GO list also has a column called "Corrected p-value".  This correction is needed because the software has performed thousands of significance tests.  I filtered on the "Corrected p-value" column to show only GO terms that have a corrected p value of < 0.05.  '''''How many GO terms are associated with this profile with a corrected p value < 0.05?''''' <span style="color:red">39 GO terms are associated with profile 45 with a corrected p value < 0.05.</span>
 ##* I selected 6 Gene Ontology terms from my filtered list of corrected p < 0.05.
 ##**'''''I looked up the definitions for each of the terms at [http://geneontology.org http://geneontology.org].  In my final presentation, I will discuss the biological interpretation of these GO terms.  In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms?  Also, what does this have to do with the transcription factor being deleted (for the Δgln3 and Δswi4 groups)?'''''
@@ Line 51: / Line 51: @@
 ##** In the [http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848 results] page, I clicked on the button that says "Link to detailed information about <term>, in this case "biological phase"".
 ##** The definition was on the next results page, e.g. [http://amigo.geneontology.org/amigo/term/GO:0044848 here].
-##***<span style="color:red">'''ribosome assembly''': The aggregation, arrangement and bonding together of the mature ribosome and of its subunits</span> [http://amigo.geneontology.org/amigo/term/GO:0042255]
+##***<span style="color:red">'''ribosome assembly''' (GO:0042255): The aggregation, arrangement and bonding together of the mature ribosome and of its subunits</span> [http://amigo.geneontology.org/amigo/term/GO:0042255]
-##***<span style="color:red">'''RNA modification''': The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically</span> [http://amigo.geneontology.org/amigo/term/GO:0009451]
+##***<span style="color:red">'''RNA modification''' (GO:0009451): The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically</span> [http://amigo.geneontology.org/amigo/term/GO:0009451]
-##***<span style="color:red">'''ncRNA catabolic process''': The chemical reactions and pathways resulting in the breakdown of non-coding RNA transcripts (ncRNAs). Includes the breakdown of cryptic unstable transcripts</span> [http://amigo.geneontology.org/amigo/term/GO:0034661]
+##***<span style="color:red">'''ncRNA catabolic process''' (GO:0034661): The chemical reactions and pathways resulting in the breakdown of non-coding RNA transcripts (ncRNAs). Includes the breakdown of cryptic unstable transcripts</span> [http://amigo.geneontology.org/amigo/term/GO:0034661]
-##***<span style="color:red">'''intracellular membrane-bounded organelle''': Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane</span> [http://amigo.geneontology.org/amigo/term/GO:0043231]
+##***<span style="color:red">'''intracellular membrane-bounded organelle''' (GO:0043231): Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane</span> [http://amigo.geneontology.org/amigo/term/GO:0043231]
-##***<span style="color:red">'''tRNA metabolic process''': The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established</span> [http://amigo.geneontology.org/amigo/term/GO:0006399]
+##***<span style="color:red">'''nucleoplasm''' (GO:0005654): That part of the nuclear content other than the chromosomes or the nucleolus.</span> [http://amigo.geneontology.org/amigo/term/GO:0006399]
-##***<span style="color:red">'''ribosomal subunit export from nucleus''': The directed movement of a ribosomal subunit from the nucleus into the cytoplasm. </span> [http://amigo.geneontology.org/amigo/term/GO:0000054]
+##***<span style="color:red">'''ribosomal subunit export from nucleus''' (GO:0000054): The directed movement of a ribosomal subunit from the nucleus into the cytoplasm. </span> [http://amigo.geneontology.org/amigo/term/GO:0000054]
 ====Files====