Ksherbina Week 5

Katrina Sherbina

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Assignment Description

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Week 5

Week 6

Week 7

Week 8

Week 9

Week 10

Week 11

Week 12

Week 13

Week 15

Class Journal

Week 1

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Individual Journal

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Week 10

Week 11

Other

Week 5: Database Wiki

Final Project

Team H(oo)KD Project Page

Journal Club Presentation

Project Individual Journal

Steps to Look Up Human EGFR Protein in the UniProt Database

1. Go to the UniProt Database.
2. Type the UniProt ID P00533 into the Query field in the top middle of the page.
3. Click the Search button.
4. Locate the navigation toolbar, which contains links to different sections in a light blue box with rounded corners that spans the page horizontally.
5. Click on the link Entry information to jump to that section.
   • This section contains information regarding Entry name (for quick identification), Accession Number (unique identifier for the protein), Entry history, Entry status, and Annotation program.
6. In the row of this section containing accession number information, click on the gray icon with two arrows pointing in opposite directions to expand the list of secondary accession numbers for the protein.
7. Scroll back to the top of the page.
8. Type the secondary accession number Q14225 for the protein into the Query filed in the middle of the page.
9. Click the search button.
   • You should be redirected to the page that you were already browsing through.
10. Click on the link Names in the navigation tool bar. This should take you to a section called "Names and origin".
    • This section should contain information regarding Protein names, Gene names, Organism, Taxonomic identifier, and Taxonomic lineage.
11. Click on the Enzyme Commission number, which is listed after "EC=" in the row designed "Protein names".
    • This will take you to a page in the database ExPASy which gives information regarding what is the biochemical function of human EGFR protein.
12. Return to the previous page in the UniProt database.
13. Click on the link References in the navigation tool bar. This will take you to a section listing various scholarly articles that have discussed the human EGFR protein.
14. Click on the link General annotation in the navigation tool bar.
    • This section contains various information about the protein, such as its function, subcellular location, and post-translational modifications.
15. Click on the link Cross-refs in the navigation tool bar, which will take you to a section titled "Cross-References containing links to entries regarding this protein in different types of databases.
    1. Click on the link X00588, which is the first link that appears under the header "Sequence databases". This link will take you to the EMBL database that gives various information regarding the nucleotide sequence that codes for you protein of interest.
    2. Go back to the UniProt page and the "Cross-References" section. Scroll down to the header "Family and domain bases" and click on the link IPR000494. This takes you to the InterPro database that describes the domains and functional sites that are present in a protein of interest.
    3. Go back to the UniProt page and the "Cross-References" section. Scroll down to the header "3D structure databases". Click on the link 1IVO. This takes you to the Protein Data Base, which gives you information including models of the structure of a protein of interest.
    4. Go back to the UniProt page and the "Cross-References" section. Scroll down to the header "Family and domain bases" and click on the link PF00757. This takes you to the Pfam database that describes the protein domain families, motifs, and repeats that apply to your protein of interest.
    5. Go back to the UniProt page and the "Cross-References" section. Below the header "Sequence databases", click on either the link NP_005219.2 or NM_005228.3. The first link takes you to information regarding the protein reference sequence of your protein of interest while the second takes you to the mRNA reference sequence that corresponds to the protein.
    6. Go back to the UniProt page and the "Cross-References" section. Scroll down to the header "Genome annotation databases" and click on the link 1956. This takes you to the NCBI GeneID database that gives various genomic and proteomic information regarding a gene of interest, such as gene ontology, chromosome location, phenotype, and protein interactions.
16. Go back to the UniProt page. Click on the link Ontologies in the navigation tool bar. This links to a section that gives a list of terms that describe the roles of the protein of interest.
    • Each of these terms link to a page in the UniProt database that define the term.
17. Click on the link Sequences in the navigation tool bar. This link takes you to a section that displays the amino acid sequence of the protein of interest as well as its length and mass.
    • If the protein of interest has multiple isoforms, such as the Human EGFR Protein, this section will show the aforementioned information for each of the isoforms.
18. Scroll back up to the top of the page.
19. Find the five yellow buttons on the right side of the page (toward the top of the page). Clicking on any one of these five buttons allows you to see the data presented on the page in one of five different formats: TXT, XML, RDF/XML, GFF, and FASTA.
    • Complete the following steps to view the RDF/XML file:
    1. Click on the button on which is written RDF/XML, which will download the file onto your computer.
    2. Go to the folder in which the file was saved.
    3. Right click on the file and open its Properties.
    4. Change the default program that opens this file to Internet Explorer. Save the changes.
    5. Double-click on the file to open it within the web browser.

Summary of Information on the Human EGFR Protein

The human epidermal growth factor receptor (EGFR) is a transmembrane protein and a type of tyrosine kinase, which transfers a phosphate from ATP to the amino acid tyrosine in another protein. This phosphorylation initiates numerous downstream signaling pathways. It is also capable of forming homodimers and heterodimers, which lead to its autophosphorylation allowing it to interact with other proteins. The human EGFR protein is found in different tissues and in different types of membranes, such as that of the cell, the Golgi apparatus, endoplasmic reticulum, and endosome. It is linked to both lung and ovarian cancer.

Answer to Reflection Questions

1. The purpose of this exercise was to become familiar with the UniProt database by exploring the different kinds of information it provides about the structure and function of the Human EGFR protein.
2. Through this exercise, I learned how to connect genomic, transcriptomic, and proteomic information regarding a protein of interest by navigating between different types of databases.
3. I had some difficulty understanding what was the function of some of the syntax of the RDF/XML file.