Ckaplan Week 10 - Revision history

Ckapla12: conclusion

2024-04-04T03:07:06Z

conclusion

Ckapla12: linking to andrew's page

2024-04-04T03:03:47Z

linking to andrew's page

Ckapla12: cold shock analysis

2024-04-04T03:00:29Z

cold shock analysis

Ckapla12: signature

2024-04-04T02:57:08Z

signature

Ckapla12: adding sources

2024-04-04T02:56:31Z

adding sources

Ckapla12: adding reference and acknowledgements

2024-04-04T02:53:40Z

adding reference and acknowledgements

Ckapla12: format

2024-04-04T02:52:17Z

format

Ckapla12: defining go terms

2024-04-04T02:51:52Z

defining go terms

Ckapla12: creating question

2024-04-04T02:38:44Z

creating question

Ckapla12: adding edges

2024-04-03T19:41:49Z

adding edges

← Older revision		Revision as of 03:07, 4 April 2024
Line 103:		Line 103:

	I think the cells are altering their gene expression to handle the stress of cold shock, involving genes for ribosomal subunits, RNA processing, nucleic acid binding, and nuclear organization. Deleting a key transcription factor that controls these genes hinders the cell's cold adaptation, affecting protein synthesis and vital cellular functions necessary for survival.		I think the cells are altering their gene expression to handle the stress of cold shock, involving genes for ribosomal subunits, RNA processing, nucleic acid binding, and nuclear organization. Deleting a key transcription factor that controls these genes hinders the cell's cold adaptation, affecting protein synthesis and vital cellular functions necessary for survival.
		+
		+	===Conclusion===
		+	In conclusion, the analysis of microarray data, particularly focusing on profile 45, gave information on how cells react to cold shock. We found a significant association of 406 genes with this profile, surpassing the expected 29.9, indicating a strong response. The presence of 44 green genes, including key regulators like Gln3p and Cin5p, emphasizes its importance in cold adaptation. Additionally, our Gene Ontology analysis revealed terms related to crucial cellular processes, indicating a comprehensive adaptation to cold stress. Once Dr. Dahlquist runs our data we will know more.

	===Acknowledgments===		===Acknowledgments===

@@ Line 106: / Line 106: @@
 ===Acknowledgments===
-I worked with Andrew multiple times in and out of class throughout the week. He helped me if I got lost or behind in class. We communicated over message for any questions. Dr. Dahlquist assisted us in class.
+I worked with [[User:Asandle1| Andrew Sandler]] multiple times in and out of class throughout the week. He helped me if I got lost or behind in class. We communicated over message for any questions. Dr. Dahlquist assisted us in class.
 ===References===

← Older revision		Revision as of 03:00, 4 April 2024
Line 101:		Line 101:

	GO:0000055 "The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm." Source: GOC:mah https://amigo.geneontology.org/amigo/medial_search?q=GO%3A0000055		GO:0000055 "The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm." Source: GOC:mah https://amigo.geneontology.org/amigo/medial_search?q=GO%3A0000055
		+
		+	I think the cells are altering their gene expression to handle the stress of cold shock, involving genes for ribosomal subunits, RNA processing, nucleic acid binding, and nuclear organization. Deleting a key transcription factor that controls these genes hinders the cell's cold adaptation, affecting protein synthesis and vital cellular functions necessary for survival.

	===Acknowledgments===		===Acknowledgments===

← Older revision		Revision as of 02:57, 4 April 2024
Line 115:		Line 115:

	http://geneontology.org.		http://geneontology.org.
		+
		+	Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
		+	[[User:Ckapla12\|Ckapla12]] ([[User talk:Ckapla12\|talk]]) 19:57, 3 April 2024 (PDT)



	{{ckaplan}}		{{ckaplan}}

@@ Line 90: / Line 90: @@
 *Select 6 Gene Ontology terms and give definitions:
-GO:0000027 "The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit." Source: GOC:jl, PMID:30467428
+GO:0000027 "The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit." Source: GOC:jl, PMID:30467428 https://amigo.geneontology.org/amigo/term/GO:0000027
-GO:0034475 "Any process involved in forming the mature 3' end of a U4 snRNA molecule." Source: GOC:mah
+GO:0034475 "Any process involved in forming the mature 3' end of a U4 snRNA molecule." Source: GOC:mah https://amigo.geneontology.org/amigo/medial_search?q=GO%3A0034475
-GO:0003676 "Binding to a nucleic acid." Source: GOC:jl
+GO:0003676 "Binding to a nucleic acid." Source: GOC:jl https://amigo.geneontology.org/amigo/medial_search?q=GO%3A0003676
-GO:0019843 "Binding to a ribosomal RNA." Source: GOC:jl
+GO:0019843 "Binding to a ribosomal RNA." Source: GOC:jl https://amigo.geneontology.org/amigo/medial_search?q=GO%3A0019843
-GO:0005654 "That part of the nuclear content other than the chromosomes or the nucleolus." Source: GOC:ma, ISBN:0124325653
+GO:0005654 "That part of the nuclear content other than the chromosomes or the nucleolus." Source: GOC:ma, ISBN:0124325653 https://amigo.geneontology.org/amigo/medial_search?q=GO%3A0005654
-GO:0000055 "The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm." Source: GOC:mah
+GO:0000055 "The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm." Source: GOC:mah https://amigo.geneontology.org/amigo/medial_search?q=GO%3A0000055
 ===Acknowledgments===

@@ Line 104: / Line 104: @@
 ===Acknowledgments===
-I worked with Andrew in and out of class throughout the week. Dr. Dahlquist assisted us in class.
+I worked with Andrew multiple times in and out of class throughout the week. He helped me if I got lost or behind in class. We communicated over message for any questions. Dr. Dahlquist assisted us in class.
 ===References===
@@ Line 114: / Line 114: @@
 LMU BioDB 2024. (2024). Week 9. Retrieved Mar 31, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_10
 {{ckaplan}}

@@ Line 65: / Line 65: @@
 *How many GO terms are less than 0.05?
 -Started with 160- after filtering 72. Then after filtering corrected p values I got 12.
 *Why did you select this profile? In other words, why was it interesting to you?
 I selected profile 45 because I thought it was interesting because out of all off our profiles, it had the most genes.
 *How many genes belong to this profile?
 *How many genes were expected to belong to this profile?
 .9
 *What is the p value for the enrichment of genes in this profile?
 .00
 *How many significant green genes?
 I have 44 green genes
 *Are Gln3p and Cin5p present? What are the percentages?
 Gln3p	46.65%
 Cin5p	31.27%
 *Genes and edges in my network:

← Older revision		Revision as of 02:51, 4 April 2024
Line 96:		Line 96:

	*Select 6 Gene Ontology terms and give definitions:		*Select 6 Gene Ontology terms and give definitions:
		+
		+	GO:0000027 "The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit." Source: GOC:jl, PMID:30467428
		+
		+	GO:0034475 "Any process involved in forming the mature 3' end of a U4 snRNA molecule." Source: GOC:mah
		+
		+	GO:0003676 "Binding to a nucleic acid." Source: GOC:jl
		+
		+	GO:0019843 "Binding to a ribosomal RNA." Source: GOC:jl
		+
		+	GO:0005654 "That part of the nuclear content other than the chromosomes or the nucleolus." Source: GOC:ma, ISBN:0124325653
		+
		+	GO:0000055 "The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm." Source: GOC:mah

	===Acknowledgments===		===Acknowledgments===