Stephen Louie Week 5

Lab Journal

• Accessed UniProt website
• Entered Primary Ascension Number:P00533 into Query. Was taken to page P00533 (EGFR_HUMAN) with alternate name "Epidermal growth factor receptor"
• Observed "Names and origin" section. Section contains protein names with alternative names. It also contains the gene names and synonyms. The organism of interest is listed. The taxonomic identifier and its lineage is listed as well.
• Observed "References" section. Section contained list of papers and journals used in research.
• Observed "General Annotations" section. Section contained details such as functions, structure, and location.
• Accessed "Cross-references" section. Observed was was found in several databases.
  • EMBL: Contained basic sequence information on genomic DNA and mRNA. Also contained visual display of base pair sequences with specific areas of interest.
  • Interpro: Contained textual summary of protein families detailing functions, effects, and structure.
  • PDB: Contained a 3D structure of the protein with basic information of the structure's function.
  • Pfam: Contained a 3D structure of the protein. Also contained a list of internal and external database links of the protein.
  • RefSeq: Contained a list of scholarly works which pertain to the protein.
  • GeneID: Contained basic information of gene. Aslo contained summary of protein function. Contained visual of gene with detailed information on specific sequences.
• Observed "Ontologies" section. Section contained words and phrases that pertained to the protein's relevance.
• Observed "Sequence annotation(Features)" section. Section listed the Amino acid sequence and detailed what function each position affected.
• Switched interface between TXT (flat), XML (tags), RDF/XML (web), GFF (Genomic specialized), and FASTA (Sequence information) formats.

Summary

Epidermal Growth Factor Receptor is a protein of the kinase superfamily found in humans. It is a cell surface protein that binds to epidermal growth factor and translates its signal into a response. Mutants of this gene have been associated with lung cancer. It is located in the Cell membrane, ER, Golgi apparatus, and nucleus. The gene contains 1210 Amino acids.

Reflection Questions

1. The purpose of this exercise was to introduce people to the use of several biological databases and to showcase the features and content of the different websites.
2. I learned how to search and use several biological databases. I also learned how what relevant information to look for when studying a specific gene. I learned a little bit about the EGFR as well.
3. I found it slightly difficult at understanding the information I was presented. I was somewhat familiar with the content I was reading, but I couldn't understand the finer points of the data concerning the protein's functions and structure. I think this pertains to my lack in biological knowledge rather than computer knowledge.

Slouie (talk) 23:14, 26 September 2013 (PDT)