Dmadere Week 8 - Revision history

Dmadere: /* Clustering and GO Term Enrichment with Stem (Part 2) */ edited formatting

2019-10-24T07:16:11Z

‎Clustering and GO Term Enrichment with Stem (Part 2): edited formatting

2019-10-24T07:10:05Z

‎References: invoked template

2019-10-24T07:09:32Z

‎Acknowledgements: signed

2019-10-24T07:09:14Z

‎Acknowledgements: edited name

2019-10-24T07:08:44Z

‎Conclusion: added conclusion

2019-10-24T07:00:46Z

‎Purpose: bolded purpose

2019-10-24T07:00:35Z

‎Purpose: added purpose

2019-10-24T06:58:42Z

‎References: added references

2019-10-24T06:53:04Z

‎Acknowledgements: added acknowledgements

2019-10-24T06:49:50Z

‎Clustering and GO Term Enrichment with Stem (Part 2): uploaded screenshot of data

@@ Line 89: / Line 89: @@
 ===Clustering and GO Term Enrichment with Stem (Part 2)===
-'''#Prepared microarray data file for loading into STEM.'''
+'''Prepared microarray data file for loading into STEM.'''
 #*Inserted a new worksheet into Excel workbook, and named it "dCIN5_stem".
 #*Selected all of the data from your "dCIN5_ANOVA" worksheet and Paste special > paste values into "dCIN5_stem" worksheet.
@@ Line 98: / Line 98: @@
 #*Renamed the data columns with just the time and units (for example, 15m, 30m, etc.).
 #*Saved work. Then used Save As to save this spreadsheet as Text (Tab-delimited) (*.txt). Clicked OK to the warnings and close your file.
-'''#Downloaded and extracted the STEM software. Click here to go to the STEM web site.'''
+'''Downloaded and extracted the STEM software. Click here to go to the STEM web site.'''
 #*Clicked on the download link and downloaded the stem.zip file to Desktop.
 #*Unzipped the file.
@@ Line 106: / Line 106: @@
 #*Downloaded "gene_association.sgd.gz".
 #*Inside the folder, double-clicked on the stem.jar to launch the STEM program.
-'''#Ran STEM'''
+'''Ran STEM'''
 #*In section 1 (Expression Data Info) of the the main STEM interface window, clicked on the Browse... button to navigate to and select your file.
 #*Clicked on the radio button No normalization/add 0.

← Older revision		Revision as of 07:10, 24 October 2019
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	*Methodology as provided and edited from the assignment page, step-by-step instrutions, and assignment updates as listed by LMU BioDB 2019. (2019). Week 8. Retrieved October 23, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8		*Methodology as provided and edited from the assignment page, step-by-step instrutions, and assignment updates as listed by LMU BioDB 2019. (2019). Week 8. Retrieved October 23, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8
	*Gene identifiers as retrieved from [https://www.yeastgenome.org Saccharomyces Genome Database]		*Gene identifiers as retrieved from [https://www.yeastgenome.org Saccharomyces Genome Database]
		+
		+	{{Dmadere}}

@@ Line 132: / Line 132: @@
 *I worked with my homework group [[User:Imacarae|Ivy]], [[User:Msamdars|Mihir]], and [[User:Eyoung20|Emma]] this week in class to complete this assignment. We talked about the assignment in class and texted about it as well if anyone needed help.
 *'''"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."'''
 ==References==
 *Methodology as provided and edited from the assignment page, step-by-step instrutions, and assignment updates as listed by LMU BioDB 2019. (2019). Week 8. Retrieved October 23, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8
 *Gene identifiers as retrieved from [https://www.yeastgenome.org Saccharomyces Genome Database]

@@ Line 130: / Line 130: @@
 ==Acknowledgements==
-*I worked with my homework group [[User:Imacarae|Ivy]], [[User:Msamdarshi|Mihir]], and [[User:Eyoung20|Emma]] this week in class to complete this assignment. We talked about the assignment in class and texted about it as well if anyone needed help.
+*I worked with my homework group [[User:Imacarae|Ivy]], [[User:Msamdars|Mihir]], and [[User:Eyoung20|Emma]] this week in class to complete this assignment. We talked about the assignment in class and texted about it as well if anyone needed help.
 *'''"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."'''

← Older revision		Revision as of 07:08, 24 October 2019
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	==Conclusion==		==Conclusion==
		+	From performing many different statistical analyses, the gene expressions were investigated to determine if the gene expression change in strain dCIN5 was significantly different from zero based on their calculated p-values. In looking at the analysis thus far, many of the genes present in dCIN were able to change their gene expression after cold shock based on their average Log fold changes overtime. Although not finished yet, the p-values calculated so far have shownthat at least 2300 of the genes expressed exhibited a p-value less than 0.05, indicating there was a significant difference from zero at any time point.

	==Acknowledgements==		==Acknowledgements==

@@ Line 1: / Line 1: @@
 ==Purpose==
-The purpose of this experiment was to analyze microarray data from ''Saccharomyces'' and see their change in gene expression after undergoing and recovering from cold shock.
+'''The purpose of this experiment was to analyze microarray data from ''Saccharomyces'' and see their change in gene expression after undergoing and recovering from cold shock.'''
 ==Method/Results==

← Older revision		Revision as of 07:00, 24 October 2019
Line 1:		Line 1:
	==Purpose==		==Purpose==
		+	The purpose of this experiment was to analyze microarray data from ''Saccharomyces'' and see their change in gene expression after undergoing and recovering from cold shock.

	==Method/Results==		==Method/Results==

← Older revision		Revision as of 06:58, 24 October 2019
Line 132:		Line 132:

	==References==		==References==
		+	*Methodology as provided and edited from the assignment page, step-by-step instrutions, and assignment updates as listed by LMU BioDB 2019. (2019). Week 8. Retrieved October 23, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8
		+	*Gene identifiers as retrieved from [https://www.yeastgenome.org Saccharomyces Genome Database]

← Older revision		Revision as of 06:53, 24 October 2019
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	==Acknowledgements==		==Acknowledgements==
		+	*I worked with my homework group [[User:Imacarae\|Ivy]], [[User:Msamdarshi\|Mihir]], and [[User:Eyoung20\|Emma]] this week in class to complete this assignment. We talked about the assignment in class and texted about it as well if anyone needed help.
		+	*'''"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."'''

	==References==		==References==