Johnllopez Week 10 - Revision history

Johnllopez616: /* Deliverables in One Convenient Place */ Corrected first link

2017-11-07T07:40:12Z

‎Deliverables in One Convenient Place: Corrected first link

Johnllopez616: Added an area for deliverables

2017-11-07T07:39:41Z

Added an area for deliverables

Johnllopez616: /* Preparing My Microarray Data File for Loading into STEM */ Changed the link location of the spreadsheets

2017-11-07T07:35:57Z

‎Preparing My Microarray Data File for Loading into STEM: Changed the link location of the spreadsheets

Johnllopez616: /* Preparing My Microarray Data File for Loading into STEM */ Declared that I uploaded it as a package

2017-11-07T07:26:06Z

‎Preparing My Microarray Data File for Loading into STEM: Declared that I uploaded it as a package

Johnllopez616: /* Acknowledgements and References */ Added my acknowledgements and references

2017-11-07T05:17:51Z

‎Acknowledgements and References: Added my acknowledgements and references

Johnllopez616: Added the conclusion

2017-11-07T05:07:52Z

Added the conclusion

Johnllopez616: Uploaded my GO and Gene tables, powerpoint, spreadsheets, and .txt files

2017-11-06T20:05:46Z

Uploaded my GO and Gene tables, powerpoint, spreadsheets, and .txt files

Johnllopez616: Added the definitions

2017-11-06T19:47:27Z

Added the definitions

Johnllopez616: Put a lot of information into "analyzing and interpreting STEM results"

2017-11-06T19:33:16Z

Put a lot of information into "analyzing and interpreting STEM results"

Johnllopez616: Explained how I prepared the document for STEM

2017-11-06T18:28:07Z

Explained how I prepared the document for STEM

@@ Line 38: / Line 38: @@
 ===Deliverables in One Convenient Place===
-*[Media: JL BIOL367 Fall2017 Dahlquist-microarray-data-master 20171017.zip | Spreadsheets]]
+*[[Media: JL BIOL367 Fall2017 Dahlquist-microarray-data-master 20171017.zip | Spreadsheets]]
 *[[Media:JohnLopezStem.zip | Powerpoint]]
 *[[Media:JL Gene Tables.zip | Gene Tables]]

@@ Line 6: / Line 6: @@
 #I then deleted all of the columns except for the Average Log Fold change columns at the timepoints. I renamed the columns with just time and units. This would be used for analyzing the timepoints in STEM later on.
 #In addition, to avoid complications with the STEM software, I replaced any values with the error #DIV/0! with a blank string. There were 40 replacements made.
-#I saved the spreadsheets as usual, then I saved it as a .txt file, which you can see [[[[Media: JL BIOL367 Fall2017 Dahlquist-microarray-data-master 20171017.zip | in this package]].
+#I saved the spreadsheets as usual, then I saved it as a .txt file, which you can see [[Media: JL BIOL367 Fall2017 Dahlquist-microarray-data-master 20171017.zip | in this package]].
 ===Downloading and Extracting STEM Software / Running STEM===
@@ Line 36: / Line 36: @@
 ===Conclusion===
 This week's lab excercise involved analyizng a set of yeast genes and their expression changes to cold shock to show which genes change significantly when exposed to cold shock. To do this, we had to first filter out every gene that had a B-H Modified p-value that was not less than .05. This meant that we would only be looking at the genes that had a significantly low p-value, meaning these genes would genuinely have an expression change most likely to the cold shock. To see which genes had similar patterns in expression changes due to cold shock, I used a software called Short Time-series Expression Miner, or STEM. STEM was easily able to view which genes followed a common model expression profile as well as allow me to view what functions they perform. After running the genes through STEM and having STEM sort them by expression profiles, I saw how genes for certain functions reacted to cold shock. I picked six gene ontology expressions that followed profile 36 for further analysis, which would be "regulation of metabolic process", "catalytic activity, acting on RNA", "hydrolase activity, acting on ester bonds", "organelle part", "transcription, DNA-templated", and "response to chemical". All of these functions followed the same pattern of expression change when given cold shock.
 ==Acknowledgements and References==

@@ Line 6: / Line 6: @@
 #I then deleted all of the columns except for the Average Log Fold change columns at the timepoints. I renamed the columns with just time and units. This would be used for analyzing the timepoints in STEM later on.
 #In addition, to avoid complications with the STEM software, I replaced any values with the error #DIV/0! with a blank string. There were 40 replacements made.
-#I saved the spreadsheets as usual, then I saved it as a .txt file, which you can see [[Media:JL Week 10 Spreadsheets.zip | in this package]].
+#I saved the spreadsheets as usual, then I saved it as a .txt file, which you can see [[[[Media: JL BIOL367 Fall2017 Dahlquist-microarray-data-master 20171017.zip | in this package]].
 ===Downloading and Extracting STEM Software / Running STEM===

@@ Line 6: / Line 6: @@
 #I then deleted all of the columns except for the Average Log Fold change columns at the timepoints. I renamed the columns with just time and units. This would be used for analyzing the timepoints in STEM later on.
 #In addition, to avoid complications with the STEM software, I replaced any values with the error #DIV/0! with a blank string. There were 40 replacements made.
-#I saved the spreadsheets as usual, then I saved it as a .txt file, which you can see [[Media:JL Week 10 Spreadsheets.zip | here]].
+#I saved the spreadsheets as usual, then I saved it as a .txt file, which you can see [[Media:JL Week 10 Spreadsheets.zip | in this package]].
 ===Downloading and Extracting STEM Software / Running STEM===

@@ Line 41: / Line 41: @@
 ==Acknowledgements and References==
 ===Acknowledgements===
 ===References===
-  http://amigo.geneontology.org/amigo/term/GO:0019222
+  LMU BioDB 2017. (2017). Week 10. Retrieved November 6, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
-  http://amigo.geneontology.org/amigo/term/GO:0006351
+ Gene Ontology (2017). ''GO:0019222''. Retrieved November 6, 2017, from http://amigo.geneontology.org/amigo/term/GO:0019222
-  http://amigo.geneontology.org/amigo/term/GO:0044422
+  Gene Ontology (2017). ''GO:0006351''. Retrieved November 6, 2017, fromhttp://amigo.geneontology.org/amigo/term/GO:0006351
-  http://amigo.geneontology.org/amigo/term/GO:0016788
+  Gene Ontology (2017). ''GO:0044422''. Retrieved November 6, 2017, fromhttp://amigo.geneontology.org/amigo/term/GO:0044422
-  http://amigo.geneontology.org/amigo/term/GO:0140098
+  Gene Ontology (2017). ''GO:0016788''. Retrieved November 6, 2017, fromhttp://amigo.geneontology.org/amigo/term/GO:0016788
-  http://amigo.geneontology.org/amigo/term/GO:0042221
+  Gene Ontology (2017). ''GO:0140098''. Retrieved November 6, 2017, fromhttp://amigo.geneontology.org/amigo/term/GO:0140098

@@ Line 6: / Line 6: @@
 #I then deleted all of the columns except for the Average Log Fold change columns at the timepoints. I renamed the columns with just time and units. This would be used for analyzing the timepoints in STEM later on.
 #In addition, to avoid complications with the STEM software, I replaced any values with the error #DIV/0! with a blank string. There were 40 replacements made.
-#I saved the spreadsheets as usual, then I saved it as a .txt file, which you can see [insert here].
+#I saved the spreadsheets as usual, then I saved it as a .txt file, which you can see [[Media:JL Week 10 Spreadsheets.zip | here]].
@@ Line 17: / Line 17: @@
 ===Viewing and Saving STEM Results===
 #After changing the Interface Options to say "X-axis scale should be based on real time", I took a screenshot of the "All STEM Profiles(1)" window, and placed it into the powerpoint given in the next step.
-#[insert here | The following] powerpoint contains screenshots of each of the individual colored boxes, which meant that these p-values within that color have a statistically significant number of assigned genes.
+#[[Media:JohnLopezStem.zip | The following]] powerpoint contains screenshots of each of the individual colored boxes, which meant that these p-values within that color have a statistically significant number of assigned genes.
-#[insert here | This] .zip file contains a series of the genes belonging to each individual significant profile.
+#[[Media:JL Gene Tables.zip | This]] .zip file contains a series of the genes belonging to each individual significant profile.
-#[insert here | This] .zip file contains a series of the gene ontology terms belonging to each individual significant profile.
+#[[Media: JL GO Tables.zip | This]] .zip file contains a series of the gene ontology terms belonging to each individual significant profile.
 ===Analyzing and Interpreting STEM Results===
 # I chose profile 36 to answer the following questions. I found 36 to be the most interesting because of the drastic expression changes at 30m, 90m, and 120m when the expression changes go from positive, to negative, then to positive again.

@@ Line 28: / Line 28: @@
 # After filtering the GO terms associated with profile 36 to have a corrected p-value > .05, I discovered that 133 of them were associated with it.
 # I then selected the following terms from my filtered list: "regulation of metabolic process", "catalytic activity, acting on RNA", "hydrolase activity, acting on ester bonds", "organelle part", "transcription, DNA-templated", and "response to chemical".
 ===Summary===
 ==Acknowledgements and References==
 ===Acknowledgements===
 ===References===

@@ Line 4: / Line 4: @@
 #I modified this further by renaming the header "Master_Index" column to "SPOT", "ID" to "Gene Symbol", and deleting the "Standard_Name" column.
 #I filtered the data on the B-H corrected p-value column to be greater than 0.05, and deleted all the data in the header row. Once I undid the filter, this ensured that all of the genes within the data set would have a B-H corrected p-value of <.05. The result was 2794 genes remaining.
-#I then deleted all of the columns except for the Average Log Fold change columns at the timepoints. This would be used for [insert use] later on.
+#I then deleted all of the columns except for the Average Log Fold change columns at the timepoints. I renamed the columns with just time and units. This would be used for analyzing the timepoints in STEM later on.
-#I saved the spreadsheets as usal, then I saved it as a .txt file, which you can see [insert here].
+#In addition, to avoid complications with the STEM software, I replaced any values with the error #DIV/0! with a blank string. There were 40 replacements made.