Week 3 Partner Project - Revision history

Jnimmers: Add DNA and protein sequence

2019-09-17T21:54:15Z

Add DNA and protein sequence

Jnimmers: Fixed Hyperlinks

2019-09-17T21:39:51Z

Fixed Hyperlinks

Jnimmers: Answered first few question

2019-09-17T21:39:08Z

Answered first few question

Jnimmers: Deleted HW partners

2019-09-17T21:24:05Z

Deleted HW partners

Jnimmers: Added Week 3 instruction

2019-09-17T21:23:49Z

Added Week 3 instruction

Jnimmers at 21:23, 17 September 2019

2019-09-17T21:23:20Z

Jnimmers: Created page

2019-09-17T18:00:31Z

Created page

New page

To choose your gene, visit the Saccharomyces Genome Database (SGD), a model organism database that aims to be a one-stop shop for yeast data.
You can search for a gene or protein in the search field or browse the resources at the site through the various tabs. If you do not already have a gene in mind that you want to find, the curators at SGD maintain a blog to highlight interesting research. Browse through the Research Spotlights or Yeast and Human Disease categories for inspiration.
You may not use the same gene as another group. Gene choices are first-come, first-served. To claim your gene, edit this page, listing the gene you have chosen next to the names of you and your homework partners.
Once you have identified your gene, you will look it up in four different databases and create a summary of what you have learned about your gene on you and our partner's wiki page. The four databases are:
SGD itself
NCBI Gene Database
Ensembl
UniProt
The summary should be one paragraph about the function of your gene based on what you have read in each of the four databases. This is one paragraph that synthesizes information, not one paragraph per database.
Provide the following additional information about your gene on your wiki page:
What is the standard name, systematic name, and name description for your gene (from SGD)?
What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
Provide hyperlinks to the specific pages for your gene in each of the above databases.
What is the DNA sequence of your gene?
What is the protein sequence corresponding to your gene?
Go to the ExPASy tool and translate the DNA sequence of your gene. Which reading frame encodes the protein sequence? Take a screenshot of your results, display it on your wiki page, and state which frame it is.
What is the function of your gene?
What was different about the information provided about your gene in each of the parent databases?
Were there differences in content, the information or data itself?
Were there differences in presentation of the information?
Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
Please make the image something scientific (not like the random images seen on the SGD blog posts).
If a 3D structure of the protein your gene encodes is available, you can choose to embed a rotating image of the structure on your page using the FirstGlance in Jmol software. This is optional, a different static image would be OK, too.
Include Acknowledgments and References sections on your wiki page. Both partners should sign the Academic Honesty statement with their wiki signatures.
You need to cite the specific database page from which you derived your information for each of the questions.
When answering the free-form questions, be sure to paraphrase.

@@ Line 39: / Line 39: @@
 *[https://www.ncbi.nlm.nih.gov/gene/854260  NCBI]
 ## What is the DNA sequence of your gene?
 ## What is the protein sequence corresponding to your gene?
 ##* Go to the [https://web.expasy.org/translate/ ExPASy tool] and translate the DNA sequence of your gene.  Which reading frame encodes the protein sequence?  Take a screenshot of your results, display it on your wiki page, and state which frame it is.
 ## What is the function of your gene?

@@ Line 34: / Line 34: @@
 A. SGD:S000005619, NCBI: 854260, Ensemble: R64-1-1:BK006948.2, UniPort: 559292
 ##* Provide hyperlinks to the specific pages for your gene in each of the above databases.
-*[[https://www.yeastgenome.org/locus/S000005619#overview | SGD]]
+*[https://www.yeastgenome.org/locus/S000005619#overview  SGD]
-*[[https://www.uniprot.org/uniprot/Q12275 | UniPort]]
+*[https://www.uniprot.org/uniprot/Q12275  UniPort]
-*[[https://uswest.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YOR093C;r=XV:497506-502452;t=YOR093C_mRNA | Ensembl]]
+*[https://uswest.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YOR093C;r=XV:497506-502452;t=YOR093C_mRNA  Ensembl]
-*[[https://www.ncbi.nlm.nih.gov/gene/854260 | NCBI]]
+*[https://www.ncbi.nlm.nih.gov/gene/854260  NCBI]
 ## What is the DNA sequence of your gene?
 ## What is the protein sequence corresponding to your gene?

@@ Line 30: / Line 30: @@
 # Provide the following additional information about your gene on your wiki page:
 ## What is the standard name, systematic name, and name description for your gene (from SGD)?
 ## What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
 ##* Provide hyperlinks to the specific pages for your gene in each of the above databases.
 ## What is the DNA sequence of your gene?
 ## What is the protein sequence corresponding to your gene?

@@ Line 7: / Line 7: @@
 ** Link to this assignment from your journal entry.
 ** Don't forget to add the "Journal Entry" category to the end of your wiki page.
 === Paper and Pencil Assignment ===

← Older revision		Revision as of 21:23, 17 September 2019
Line 58:		Line 58:
	##* You need to cite the specific database page from which you derived your information for each of the questions.		##* You need to cite the specific database page from which you derived your information for each of the questions.
	##* When answering the free-form questions, be sure to paraphrase.		##* When answering the free-form questions, be sure to paraphrase.
		+
		+	Were there differences in presentation of the information?
		+	Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
		+	Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
		+	Please make the image something scientific (not like the random images seen on the SGD blog posts).
		+	If a 3D structure of the protein your gene encodes is available, you can choose to embed a rotating image of the structure on your page using the FirstGlance in Jmol software. This is optional, a different static image would be OK, too.
		+	Include Acknowledgments and References sections on your wiki page. Both partners should sign the Academic Honesty statement with their wiki signatures.
		+	You need to cite the specific database page from which you derived your information for each of the questions.
		+	When answering the free-form questions, be sure to paraphrase.

@@ Line 1: / Line 1: @@
-To choose your gene, visit the Saccharomyces Genome Database (SGD), a model organism database that aims to be a one-stop shop for yeast data.
+== Individual Journal Assignment ==
 You can search for a gene or protein in the search field or browse the resources at the site through the various tabs. If you do not already have a gene in mind that you want to find, the curators at SGD maintain a blog to highlight interesting research. Browse through the Research Spotlights or Yeast and Human Disease categories for inspiration.
-You may not use the same gene as another group. Gene choices are first-come, first-served. To claim your gene, edit this page, listing the gene you have chosen next to the names of you and your homework partners.
+* Store this journal entry as "''gene name'' Week 3" (i.e., this is the text to place between the square brackets when you link to this page).  Each partner will contribute to '''one''' journal page for this week.
-Once you have identified your gene, you will look it up in four different databases and create a summary of what you have learned about your gene on you and our partner's wiki page. The four databases are:
+* Create the following set of links. '''''(HINT: These links should all be in your personal template that you created for the [[Week 1 | Week 1 Assignment]]; you should then simply invoke your template on each new journal entry.)'''''  Each partner would invoke their template on the shared page.
-SGD itself
+** Link to your journal entry from your user page.
-NCBI Gene Database
+** Link back from your journal entry to your user page.
-Ensembl
+** Link to this assignment from your journal entry.
-UniProt
+** Don't forget to add the "Journal Entry" category to the end of your wiki page.
 The summary should be one paragraph about the function of your gene based on what you have read in each of the four databases. This is one paragraph that synthesizes information, not one paragraph per database.
-Provide the following additional information about your gene on your wiki page:
+=== Homework Partners ===
 What is the standard name, systematic name, and name description for your gene (from SGD)?
-What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
+You are expected to work with your homework partner, in order to complete the assignment. '''''For this week, you and your partner will work together on one wiki page.''''' Homework partners for this week are: You must give the details of the interaction with your partner in the [[Week_1#Acknowledgments | Acknowledgments section]] of your journal assignment.  Homework partners for this week are:
 Provide hyperlinks to the specific pages for your gene in each of the above databases.
-What is the DNA sequence of your gene?
+* Christina and Naomi : RAD53 / YPL153C
-What is the protein sequence corresponding to your gene?
+* DeLisa and Joey: CMR2 / YOR093C
-Go to the ExPASy tool and translate the DNA sequence of your gene. Which reading frame encodes the protein sequence? Take a screenshot of your results, display it on your wiki page, and state which frame it is.
+* Emma and Michael
-What is the function of your gene?
+* Ivy and Aby: HSF1/YGL073W
-What was different about the information provided about your gene in each of the parent databases?
+* Kaitlyn and Iliana ILT1/YDR090C
-Were there differences in content, the information or data itself?
+* Marcus and David: cyclin dependent kinase 2 (CDC28/YBR160W)
-Were there differences in presentation of the information?
+* Mihir and Jonar: FAS2 / YPL231W
 Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
-Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
+=== Paper and Pencil Assignment ===
 Please make the image something scientific (not like the random images seen on the SGD blog posts).
-If a 3D structure of the protein your gene encodes is available, you can choose to embed a rotating image of the structure on your page using the FirstGlance in Jmol software. This is optional, a different static image would be OK, too.
+You will turn in ''individually'' the completed [[Media:BIOL367_Fall2019_GeneticCode-CentralModel-2.pdf | paper and pencil assignment]] that was handed out in class on Thursday, 9/12/19.  The paper copy is due at the beginning of class on Thursday, 9/19/19.
 Include Acknowledgments and References sections on your wiki page. Both partners should sign the Academic Honesty statement with their wiki signatures.
-You need to cite the specific database page from which you derived your information for each of the questions.
+=== “My Favorite Gene” ===
 When answering the free-form questions, be sure to paraphrase.