Difference between revisions of "Mpetredi Week 5"
From LMU BioDB 2013
(added notes about some sections) |
(Added more info about cross-refs) |
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#Clicked the 2.7.10.1 hyperlink. | #Clicked the 2.7.10.1 hyperlink. | ||
#*Redirected to http://enzyme.expasy.org/EC/2.7.10.1. This link describes the receptor "protein-tyrosine kinase." | #*Redirected to http://enzyme.expasy.org/EC/2.7.10.1. This link describes the receptor "protein-tyrosine kinase." | ||
| − | |||
| − | |||
#Located Quick Search Box (Under Query) | #Located Quick Search Box (Under Query) | ||
#Noticed the quick links around the top of the page, under the Quick Search box. Each link directs you to a specific section of the entry | #Noticed the quick links around the top of the page, under the Quick Search box. Each link directs you to a specific section of the entry | ||
| − | #*[[http://www.uniprot.org/uniprot/P00533#section_name Names]]: | + | #*[[http://www.uniprot.org/uniprot/P00533#section_name Names]]: States all the ways P00533 can be identified |
| − | #*[[http://www.uniprot.org/uniprot/P00533#section_attribute Attributes]] | + | #*[[http://www.uniprot.org/uniprot/P00533#section_attribute Attributes]]: States the sequence length, sequence status, sequence processing, and protein existence of a subject. |
#*[[http://www.uniprot.org/uniprot/P00533#section_comments General annotation]]: AKA Comments. Provides additional, brief information about the function, catalytic activity, enzyme regulation, subunit structure, sub cellular location, tissue specificity, post-translational modification, involvement in decease, and sequence similarities. Check this section first to get a basic idea of a subject before proceeding to the more fully detailed information. | #*[[http://www.uniprot.org/uniprot/P00533#section_comments General annotation]]: AKA Comments. Provides additional, brief information about the function, catalytic activity, enzyme regulation, subunit structure, sub cellular location, tissue specificity, post-translational modification, involvement in decease, and sequence similarities. Check this section first to get a basic idea of a subject before proceeding to the more fully detailed information. | ||
#*[[http://www.uniprot.org/uniprot/P00533#section_terms Ontologies]] | #*[[http://www.uniprot.org/uniprot/P00533#section_terms Ontologies]] | ||
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#*[[http://www.uniprot.org/uniprot/P00533#section_ref References]]: Contains all materials used when compiling the report on P00533. | #*[[http://www.uniprot.org/uniprot/P00533#section_ref References]]: Contains all materials used when compiling the report on P00533. | ||
#*[[http://www.uniprot.org/uniprot/P00533#section_web Web links]] | #*[[http://www.uniprot.org/uniprot/P00533#section_web Web links]] | ||
| − | #*[[http://www.uniprot.org/uniprot/P00533#section_x-ref Cross-refs]] | + | #*[[http://www.uniprot.org/uniprot/P00533#section_x-ref Cross-refs]]: This section provides other links pertaining to the same subject. Each link performs a different function from the others. |
| + | #**[[http://www.ebi.ac.uk/ena/data/view/X00588 EMBL]]: Mostly contains raw data and results presented in an outline format. | ||
| + | #**[[http://www.ebi.ac.uk/interpro/entry/IPR000494 InterPro]]: Information is presented in paragraph form with many descriptors. | ||
| + | #**[[http://www.ebi.ac.uk/pdbe-srv/view/entry/2EB3 PDB]]: Displays virtual models of the subject (P00533 in this case) and mentions what certain colors on the model indicates. | ||
| + | #**[[http://pfam.sanger.ac.uk/family/PF00757 Pfam]]: Also displays a virtual model of the subject, but with less detail than PDB. It does provide other links to similar subjects and databases related to the searched subject | ||
| + | #**[[http://www.ncbi.nlm.nih.gov/protein/NP_005219.2 RefSeq]]: Directed to NCBI that contains similar or the information as uniprot, but not structured as easily as uniprot. | ||
| + | #**[[http://www.ncbi.nlm.nih.gov/gene/1956 GeneID]]: Also directed to NCBI, but the presented information has less content and looks cleaner. Contains many links to other pages on and off NCBI. | ||
#*[[http://www.uniprot.org/uniprot/P00533#section_general Entry info]] | #*[[http://www.uniprot.org/uniprot/P00533#section_general Entry info]] | ||
#*[[http://www.uniprot.org/uniprot/P00533#section_documents Documents]] | #*[[http://www.uniprot.org/uniprot/P00533#section_documents Documents]] | ||
Revision as of 21:11, 26 September 2013
UniProt Exercise Journal
- Navigated to http://www.uniprot.org instead of http://web.expasy.org/docs/swiss-prot_guideline.html as per week 5 instruction
- Typed P00533 in search box on uniprot website.
- Sent to http://www.uniprot.org/uniprot/P00533. Link describes Epidermal growth factor receptor (EGFR).
- Clicked the 2.7.10.1 hyperlink.
- Redirected to http://enzyme.expasy.org/EC/2.7.10.1. This link describes the receptor "protein-tyrosine kinase."
- Located Quick Search Box (Under Query)
- Noticed the quick links around the top of the page, under the Quick Search box. Each link directs you to a specific section of the entry
- [Names]: States all the ways P00533 can be identified
- [Attributes]: States the sequence length, sequence status, sequence processing, and protein existence of a subject.
- [General annotation]: AKA Comments. Provides additional, brief information about the function, catalytic activity, enzyme regulation, subunit structure, sub cellular location, tissue specificity, post-translational modification, involvement in decease, and sequence similarities. Check this section first to get a basic idea of a subject before proceeding to the more fully detailed information.
- [Ontologies]
- [Interactions]
- [Alt products]
- [Sequence annotation]
- [Sequences]
- [References]: Contains all materials used when compiling the report on P00533.
- [Web links]
- [Cross-refs]: This section provides other links pertaining to the same subject. Each link performs a different function from the others.
- [EMBL]: Mostly contains raw data and results presented in an outline format.
- [InterPro]: Information is presented in paragraph form with many descriptors.
- [PDB]: Displays virtual models of the subject (P00533 in this case) and mentions what certain colors on the model indicates.
- [Pfam]: Also displays a virtual model of the subject, but with less detail than PDB. It does provide other links to similar subjects and databases related to the searched subject
- [RefSeq]: Directed to NCBI that contains similar or the information as uniprot, but not structured as easily as uniprot.
- [GeneID]: Also directed to NCBI, but the presented information has less content and looks cleaner. Contains many links to other pages on and off NCBI.
- [Entry info]
- [Documents]
- [Customize]: Use this to change the default ordering of sections.
P00533, or Epidermal Growth Factor Receptor: A Brief Summary
(My brief summary will go here)
Individual Assignment Response to Questions
- The purpose of this exercise was to become more familiar with the layout of information presented by UniProt for a particular sequence or protein.
- I learned how to locate relevant information pertaining to this course.
- I currently don't know how I will utilize the information for a certain sequence or protein in my project for this course.
