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When working with transcriptomic data sets, the first step that most researchers will typically conduct is differential gene expression analysis. Although this is an essential first step, it is limited in the sense that it will only inform researchers which genes are up or down-regulated, relative to a control condition.

In some cases, it may be more intuitive to visualize differential expression analysis results in a more realistic context. Pathway maps are collections of enzymatic reactions, metabolites, and intermediates which have been compiled into a “map” to depict general cellular and metabolic processes.

There are many different repositories that

have compiled such maps to be used with a broad array of different organisms, some of the most popular being the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Escher Visualizations.

In this assignment, we will demonstrate pathway visualizations of KEGG maps with differential expression data sets using a web tool called pathView – it also has an R-compatible package; however, we will use the web tool for simplicity, as this is not a computer science course.

The results from differential gene expression analysis can be used as input for path view and the user selects the respective pathway(s) which they would be interested in when conducting their own research. pathView supports visualization of gene expression data (the gene identifiers need to be compatible with the organism being studied) as well as metabolite data:

Screen Shot 2021-04-29 at 7.18.07 PM.png

The color-coated legends depict enzymatic or metabolite changes on the Log2FoldChange scale, relative to a control condition; enzymatic reactions highlighted in red imply more activity, relative to the control, while enzymatic reactions highlighted in green symbolize a reduction in activity, relative to a control.

For this assignment, please navigate to the pathView user home (link below) and select one of the examples (there are 4 of them). Once you have clicked on one of the examples, choose 3 pathways (not including propanoate metabolism) and run the analysis using the demo data sets which have already been pre-loaded. Take a screenshot of the three pathway visualizations and compile them into a word document or PDF file to submit for assignment 2.

pathView Web Home (Links to an external site.)

EditEditEditEditFor your final notebook check, please submit a Word or PDF document with some notes describing the advantages that pathway visualization has over standard differential gene expression analysis. How might a researcher use pathway visualizations after conducting differential gene expression analysis to further their research? Screen Shot 2021-04-29 at 7.30.18 PM.png


For your final notebook check, please submit a Word or PDF document with some notes describing the advantages that pathway visualization has over standard differential gene expression analysis. How might a researcher use pathway visualizations after conducting differential gene expression analysis to further their research?


assignment 2


For your final assignment of Online Part 3, you will design your own hypothetical experiment and write a short prompt to describe how you would go about conducting such an experiment from start to finish, including how you would grow cells, how to prepare them for RNA-seq, and what you would do after you have obtained raw gene counts. Get creative with this assignment – its your chance to think like a scientist in a real-world scenario.

If you need a general idea of how a prompt should look, I have attached a short sample prompt:

download

Please submit a minimum 300 word PDF or Word document depicting your experiment by Sunday 5/2 at 11:59 PST.



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San Diego State University Ad

Hello there, I need help answering my question. I have the prompt at the bottom below word(Starting )so go over it and let me know if you have any questions. Before reading the prompt, I just want to let you know that your working on the small part, not the whole assignment.

my group and I chose to do art and math,

* the only thing I want you to do is this part

(5b. Produce two to three lesson plans that explain what your project is and will do. Your lesson plan should include the following:

      • Learning outcomes for the entire project
      • Ways to build off of what students already know
      • Lesson: what will students be doing
      • Assessment: How will you know your project was successful.
      • >>>>>>>>>>>>>>>>>>>>>>>>>>>
    • I attached 2 lesson plans for you and you can get all the information from the second one. I started my lesson plan but I’m confused about how to add more so try to follow the first lesson plan. again, the second lesson plan is mine and might not be right so follow the first one, please. You can add or take off things from it. the lesson plan is about teaching addition to first and second grades.
    • again, I sent you the first lesson plan as an example and the second one is mine that I started and I just need your help to gather all the ideas together.
    • I sent you an attachment that has my classmate’s lesson plan( shapes) and mine (addition) is to the bottom. I also send you the sign-in link to go over my website to do my part just like my classmates. our lesson plans are ( shapes, tesselation, and mine is addition.

Starting:

Collaborative Group Assessment

You are about to earn a Liberal Studies Bachelors degree. In so doing, you may be about to start your career in elementary or middle school education. This project encourages you to use all that you learned from the past years and beyond to put together a project that could benefit young elementary students.

You and your colleagues (a group of 3 to 5 peers) are applying for a $5,000 grant to design an educational program at a local school. To design this program, you must make it suitable and engaging for elementary and foundational middle school students.

What to do?

  1. You must work collaboratively with 3 to 5 peers.
  2. As a group, you will design an innovative school project. To do this situate your project at a real school from one of our school districts: Chula Vista School District (CVSD), La Mesa Spring Valley (LMSV), and San Diego Unified School District (SDUSD).
  3. Select a school within in one of the above mentioned school districts. The only caveat is that the school and program must serve low-income students.
  4. Once you have identified a school work collaboratively to design a program. You can generate your own program OR You can build a project based on one of the following:

5. Once you have a project to build, create the following to correspond with your project:

a. Write a project summary: Be sure to describe how many days and hours. The project should not exceed 20 hours in length.

b. Produce two to three lesson plans that explain what your project is and will do. Your lesson plan should include the following:

      • Learning outcomes for the entire project
      • Ways to build off of what students already know
      • Lesson: what will students be doing
      • Assessment: How will you know your project was successful.

6. Once you have an idea and some lesson plans, create a web page to post lesson plans and the following.

7. Create a 1 minute video about your project

8. Generate a Budget: $5,000. Your budget must include salaries, materials for activities,

9. Create infographics about the population. Learn about the school you are designing a program for. Provide information about their:

      1. the number of students
      2. ethnicity of the students
      3. languages students speak
      4. grade levels your project is targeting
      5. how many in those grade levels

10. Use theory from the modules (i.e., persistence, the brain, anti-racist teaching, and intelligence theories) to explain how the project will be effective

11. Describe the roles for each member of the group

12. Reflect on your role

13. Presentation: 5 minute pitch with 5 minute Q & A (total 10 minutes). Each person in the group must talk. The presentation must show that each member contributed equally to the development of the program.

To earn credit, please submit a Webpage url link with all the above included.

my group and I chose to do art and math,

* the only thing I want you to do is this part

(b. Produce two to three lesson plans that explain what your project is and will do. Your lesson plan should include the following:

      • Learning outcomes for the entire project
      • Ways to build off of what students already know
      • Lesson: what will students be doing
      • Assessment: How will you know your project was successful.
      • >>>>>>>>>>>>>>>>>>>>>>>>>>>
    • I attached 2 lesson plans for you and you can get all the information from the second one. I started my lesson plan but I’m confused about how to add more so try to follow the first lesson plan. again, the second lesson plan is mine and might not be right so follow the first one, please. You can add or take off things from it. the lesson plan is about teaching addition to first and second grades.
    • again, I sent you the first lesson plan as an example and the second one is mine that I started and I just need your help to gather all the ideas together.
    • I sent you an attachment that has my classmate’s lesson plan( shapes) and mine (addition) is to the bottom. I also send you the sign-in link to go over my website to do my part just like my classmates. our lesson plans are ( shapes, tesselation, and mine is addition.
    • Now, let me know if you have any other questions.

Place this order or similar order and get an amazing discount. USE Discount code “GET20” for 20% discount

Posted in Uncategorized