Eyoung20 journal week 9 - Revision history

Eyoung20: /* References */

2019-10-31T05:24:22Z

‎References

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‎Acknowledgements

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‎# Analyzing and Interpreting STEM Results: formating

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‎# Viewing and Saving STEM Results: formating

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‎Conclusion: finished conclusion

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‎Conclusion: added info

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‎Conclusion: adding info for conclusion

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‎Conclusion: working on conclusion

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‎Conclusion: added info to conclusion

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‎Conclusion: adding info to conclusion section

← Older revision		Revision as of 05:24, 31 October 2019
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	==References==		==References==
		+	LMU BioDB 2019. (2019). Week 9. Retrieved October 30, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_9
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	{{Template:eyoung20}}		{{Template:eyoung20}}

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 ==Acknowledgements==
 ==References==
 {{Template:eyoung20}}

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 ##** Upload these files to the wiki and link to them on your individual journal page.  (Note that it will be easier to [[Week_4#Compressing_and_Decompressing_Files_with_7-Zip | zip all the files together]] and upload them as one file).
-===# '''Analyzing and Interpreting STEM Results'''===
+# '''Analyzing and Interpreting STEM Results'''
 ## Select '''''one''''' of the profiles you saved in the previous step for further intepretation of the data.  I suggest that you choose one that has a pattern of up- or down-regulated genes at the cold shock timepoints.  '''''Each member of your group should choose a different profile.'''''  Answer the following:
 ##* '''''Why did you select this profile?  In other words, why was it interesting to you?'''''

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 ##** The definition will be on the next results page, e.g. [http://amigo.geneontology.org/amigo/term/GO:0044848 here].
 ##* '''''This is the stopping point for the [[Week 8]] assignment and the beginning point for Week 9'''''
-===# '''Viewing and Saving STEM Results'''===
+# '''Viewing and Saving STEM Results'''
 ## A new window will open called "All STEM Profiles (1)".  Each box corresponds to a model expression profile.  Colored profiles have a statistically significant number of genes assigned; they are arranged in order from most to least significant p value.  Profiles with the same color belong to the same cluster of profiles.  The number in each box is simply an ID number for the profile.
 ##* Click on the button that says "Interface Options...".  At the bottom of the Interface Options window that appears below where it says "X-axis scale should be:", click on the radio button that says "Based on real time".  Then close the Interface Options window.

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 GLN3 42.53% in user set, 1.54% in yeast tract, p-value = 0.0338494
 HAP4 11.49% in user set, 0.93% in yeast tract, p-value = 0.7968973
-Form this sheet the genes chosen for for visualizing the gene network on GRNsight were; Yap1, Pdr3, Pdr1, Rpn4, Gcn4, YGR067C, Nrg2, Crz1, Met31, Tec1, Sum1, Gzf3, Mss11, Xbp1, Zms1, GLN3, HAP4, and CIN5. These genes were chosen from the 5 significant genes from the yeasttract results and then the next 10 results with the lowest p-values. Then the genes GLN3, HAP4, CIN5 were added making the total 18 genes.
+Form this sheet the genes chosen for for visualizing the gene network on GRNsight were; Yap1, Pdr3, Pdr1, Rpn4, Gcn4, YGR067C, Nrg2, Crz1, Met31, Tec1, Sum1, Gzf3, Mss11, Xbp1, Zms1, GLN3, HAP4, and CIN5. These genes were chosen from the 5 significant genes from the yeasttract results and then the next 10 results with the lowest p-values. Then the genes GLN3, HAP4, CIN5 were added making the total 18 genes. There was a formatting error with the .xslx sheet which did not allow GRNsight to work with the data. No matter how many times the steps were redone the same error occurred. some outside assistance is required to help resolve this error. So the visualizing of the gene network failed.
 ==Acknowledgements==
 ==References==
 {{Template:eyoung20}}

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 ==Conclusion==
-The STEM results profile #2 was selected out of the profiles. This profile was selected due to the fact that it demonstrated both down and up trends at different cold shock time points. There are 88 genes in this profile. Of those 88 genes only 34 genes were expected to belong to this profile. The p-value for the profile was 1.0x10^-15, which means that there was a significant difference between the amount of genes that were expected and the amount that occurred.
+The STEM results profile #2 was selected out of the profiles. This profile was selected due to the fact that it demonstrated both down and up trends at different cold shock time points. There are 88 genes in this profile. Of those 88 genes only 34 genes were expected to belong to this profile. The p-value for the profile was 1.0x10^-15, which means that there was a significant difference between the amount of genes that were expected and the amount that occurred. Of the GO list for this profile there were only 6 that had a p-value less than 0.05 ; GO:0008150, GO:0003674, GO:0005575, GO:0007049, GO:0051301, and GO:0016021. Only 3 of these had a corrected p-value less than 0.05;
 GO:0008150: dopamine neurotransmitter receptor activity - Combining with the neurotransmitter dopamine and activating adenylate cyclase via coupling to Gi/Go to initiate a change in cell activity.